@article {pmid40181281,
year = {2025},
author = {Degnan, PH and Percy, DM and Hansen, AK},
title = {Coupled evolutionary rates shape a Hawaiian insect-symbiont system.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {336},
pmid = {40181281},
issn = {1471-2164},
support = {DEB 1241253//NSF/ ; 2019-70016-29066//National Institute of Food and Agriculture/ ; },
mesh = {Animals ; *Symbiosis/genetics ; *Evolution, Molecular ; Phylogeny ; Hawaii ; *Hemiptera/genetics/microbiology/classification ; Genome, Mitochondrial ; Genome, Insect ; },
abstract = {BACKGROUND: The Hawaiian Pariaconus psyllid radiation represents a unique system to study the co-evolution of nuclear, mitochondrial, and endosymbiont genomes. These psyllids, which diversified across the Hawaiian Islands during the last 3-3.5 million years vary with their ecological niches on their plant host 'Ōhi'a lehua (Metrosideros polymorpha) (free-living, open-gall, and closed-gall lifestyles) and harbor one to three beneficial bacterial endosymbionts. Co-evolutionary studies of other multi-endosymbiont insect systems have shown decoupled rates of sequence evolution between mitochondria and endosymbionts. Here we examine the evolutionary trends in Pariaconus psyllids, their mitochondria and their endosymbionts to determine if they fit this paradigm.

RESULTS: We sequenced a new Carsonella genome from the ohialoha species group (closed-gall, one symbiont), revealing a remarkable degree of gene conservation between two of the most divergent species from this diverse species group that has dispersed across multiple islands. Further, despite the rapid radiation of psyllid species, we observed complete synteny among mitochondrial genomes from all six Pariaconus species in this study, suggesting the preservation of genome structure due to strong purifying selection. Phylogenetic analyses of the nuclear, mitochondrial, and endosymbiont genomes across these six Pariaconus species revealed correlated rates of substitutions, contrary to prior reports of decoupling between mitochondrial and endosymbiont genomes in other insect systems with multiple symbiont partners. Finally, we found that free-living psyllids with three symbionts exhibited elevated mutation rates (~ 1.2-1.6x) across all genomes and elevated rates of fixation of nonsynonymous substitutions in the insect nuclear genome and one of the endosymbionts.

CONCLUSIONS: This study highlights the interplay between ecological diversification and genomic evolution in Pariaconus. Further, these data indicate that multiple endosymbiont partners alone are not sufficient to result in decoupling rates of sequence evolution. Future work on basal members of this species radiation will refine our understanding of the mechanisms shaping this dynamic insect-symbiont system and its implications for genome evolution.},
}

Animals
*Symbiosis/genetics
*Evolution, Molecular
Phylogeny
Hawaii
*Hemiptera/genetics/microbiology/classification
Genome, Mitochondrial
Genome, Insect

@article {pmid40174913,
year = {2025},
author = {Rubens, P and Mayeur, A and Chatzovoulou, K and Gigarel, N and Monnot, S and Rötig, A and Munnich, A and Frydman, N and Steffann, J},
title = {Profiling mitochondrial DNA variant segregation during human preimplantation development: a prerequisite to preimplantation genetic testing for mitochondrial DNA-related disorders.},
journal = {Human reproduction (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/humrep/deaf050},
pmid = {40174913},
issn = {1460-2350},
support = {//Association Française contre les Myopathies/ ; },
abstract = {STUDY QUESTION: Is preimplantation genetic testing for mitochondrial DNA (mtDNA) disorders (PGT-mt) feasible at early compaction and blastocyst stages?

SUMMARY ANSWER: Pathogenic mtDNA variants segregate evenly among cell types and various lineages of a given embryo during preimplantation development, supporting the relevance of genetic analyses performed on Day 4 blastomere and on Day 5 or 6 trophectoderm (TE) samples.

WHAT IS KNOWN ALREADY: PGT-mt is validated at cleavage stage (Day 3 of development). However, its feasibility at later stages is questionable, as little is known regarding the segregation of pathogenic mtDNA variants during preimplantation development. Since mtDNA replication is silenced until the blastocyst stage (Day 5 or 6), uneven mtDNA segregation between preimplantation embryo cellular lineages known as a 'bottleneck' effect, cannot be excluded, posing a challenge for PGT-mt.

STUDY DESIGN, SIZE, DURATION: We analyzed 112 'mito' embryos carrying pathogenic mtDNA variants and 28 control embryos with mtDNA polymorphism. Heteroplasmy levels were assessed in single cells of the TE, in different parts of blastocysts (inner cell mass and TE), and at three time points of development, namely cleavage (Day 3), early compaction (Day 4), and blastocyst stages (Day 5 or 6).

As part of clinical PGT, a blastomere biopsy was performed at cleavage or early compaction stages (Day 3 or 4) on 112 'mito' and 21/28 control embryos. Further analysis was carried out at Day 5 or 6 on 51 embryos deemed unsuitable for uterine transfer and donated to research. Heteroplasmy levels were determined by semi-quantitative PCR amplification of (i) the mtDNA pathogenic variants with additional enzymatic digestion or (ii) the mtDNA polymorphic hypervariable region 2.

Here, we first show that mtDNA variants segregate evenly among blastomeres during early compaction (Day 4), supporting the feasibility of PGT-mt at this stage. We also found that mtDNA ratios remain stable between cleavage and blastocyst stages. Yet, the substantial variation of heteroplasmy levels occurring among single TE cells in 1/8 embryos suggests that PGT is only feasible when at least 5-10 cells are collected by standard TE biopsy.

This study sheds light on mtDNA segregation in human preimplantation embryo development. Its limitation lies in the scarcity of the material and the small number of embryos carrying a specific pathogenic mtDNA variant. Furthermore, the study of single cells from TE was performed on control embryos only.

By supporting the relevance of blastocyst biopsy in the context of PGT for pathogenic mtDNA variants, this study contributes to the general trend of postponing the biopsy to later stages of embryonic development. However, particular attention should be paid to the number of TE cells tested. Due to the potential variation of mutant load during in utero development, a control amniocentesis for evolutive pregnancies following the transfer of heteroplasmic embryos is still recommended.

This work was funded by 'Association Française contre les Myopathies/AFM Téléthon' (22112, 24317, 28525); and EUR G.E.N.E. (No. ANR-17-EURE-0013). The authors have no competing interests to declare.

TRIAL REGISTRATION NUMBER: N/A.},
}

@article {pmid40174813,
year = {2025},
author = {Xu, J and Shen, Z and Hao, T and Su, H and Chen, M and Pan, X and Yi, Z},
title = {Exploring the evolution of anaerobes within ciliate class Prostomatea by transcriptomics.},
journal = {Molecular phylogenetics and evolution},
volume = {},
number = {},
pages = {108345},
doi = {10.1016/j.ympev.2025.108345},
pmid = {40174813},
issn = {1095-9513},
abstract = {Mitochondrion-related organelles (MROs) enable anaerobic eukaryotes to thrive in anoxic environments, and the independent ciliate lineages of anaerobes serve as excellent candidates for investigating the convergent evolutionary transition from mitochondria to MROs. Previous studies have demonstrated that the adaptations of ciliates to anaerobic conditions may be lineage-specific. However, our understanding of the diverse metabolic peculiarities of MROs is limited to a few ciliate lineages. In this study, we sequenced the transcriptomes of four anaerobic species from two genera (Apolagynus and Holophrya), which are classified within the predominantly aerobic class Prostomatea, and predicted their mitochondrial metabolism. The ecological niches of prostomatean anaerobes were mapped onto newly constructed phylogenomic trees and small subunit (SSU) rDNA trees. Results showed that paraphyletic class Prostomatea containing six clades (Clade I-Ⅵ) has a close relationship with Oligohymenophorea and Plagiopylea. Notably, all prostomatean species within Clade II are anaerobic, while anaerobes are only sporadically present in other clades. The MROs of anaerobic prostomatean species display at least two distinct phenotypes. Holophrya ovum in Clade I produces ATP by oxidative phosphorylation under aerobic conditions and via substrate-level phosphorylation via acetate: succinate CoA transferase (ASCT) and succinyl CoA synthetase (SCS) as well as adenylate kinase (AK) under anaerobic conditions. In contrast, three species of Apolagynus in Clade II possess reduced electron transport chain (ETC), and are capable of ATP generation via substrate-level phosphorylation mediated by ASCT/SCS and propionyl-CoA. Additionally, these three Apolagynus species possess [FeFe] hydrogenase probably producing H2. A comparison of the ETC pathways among various anaerobic ciliates further showed that the MROs of these organisms have originated from repeated convergent evolution. Our findings shed lights on evolutionary history of anaerobes within the ciliate class Prostomatea.},
}

@article {pmid40167337,
year = {2025},
author = {Koch, RE and Truong, CN and Reeb, HR and Joski, BH and Hill, GE and Zhang, Y and Toomey, MB},
title = {Multiple Pathways to Red Carotenoid Coloration: House Finches (Haemorhous mexicanus) Do Not Use CYP2J19 to Produce Red Plumage.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e17744},
doi = {10.1111/mec.17744},
pmid = {40167337},
issn = {1365-294X},
support = {NSF-IOS-2037735//Directorate for Biological Sciences/ ; NSF-IOS-2037739//Directorate for Biological Sciences/ ; NSF-IOS-2037741//Directorate for Biological Sciences/ ; NSF-IOS-2224556//Directorate for Biological Sciences/ ; },
abstract = {The carotenoid-based colours of birds are a celebrated example of biological diversity and an important system for the study of evolution. Recently, a two-step mechanism, with the enzymes cytochrome P450 2J19 (CYP2J19) and 3-hydroxybutyrate dehydrogenase 1-like (BDH1L), was described for the biosynthesis of red ketocarotenoids from yellow dietary carotenoids in the retina and plumage of birds. A common assumption has been that all birds with ketocarotenoid-based plumage coloration used this CYP2J19/BDH1L mechanism to produce red feathers. We tested this assumption in house finches (Haemorhous mexicanus) by examining the catalytic function of the house finch homologues of these enzymes and tracking their expression in birds growing new feathers. We found that CYP2J19 and BDH1L did not catalyse the production of 3-hydroxy-echinenone (3-OH-echinenone), the primary red plumage pigment of house finches, when provided with common dietary carotenoid substrates. Moreover, gene expression analyses revealed little to no expression of CYP2J19 in liver tissue or growing feather follicles, the putative sites of pigment metabolism in moulting house finches. Finally, although the hepatic mitochondria of house finches have high concentrations of 3-OH-echinenone, observations using fluorescent markers suggest that both CYP2J19 and BDH1L localise to the endomembrane system rather than the mitochondria. We propose that house finches and other birds that deposit 3-OH-echinenone as their primary red plumage pigment use an alternative enzymatic pathway to produce their characteristic red ketocarotenoid-based coloration.},
}

@article {pmid40141318,
year = {2025},
author = {Prado-Souza, LFLD and Ferraz, LS and Citrangulo Tortelli, T and Ribeiro, CAJ and Amaral, DTD and Arruda, DC and Oliveira, ÉA and Chammas, R and Maria-Engler, SS and Rodrigues, T},
title = {Exploiting Paradoxical Activation of Oncogenic MAPK Signaling by Targeting Mitochondria to Sensitize NRAS Mutant-Melanoma to Vemurafenib.},
journal = {International journal of molecular sciences},
volume = {26},
number = {6},
pages = {},
pmid = {40141318},
issn = {1422-0067},
support = {2021/14650-3//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 306681/2023-4//Conselho Nacional de Pesquisa e Desenvolvimento Científico e Tecnológico/ ; 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; },
mesh = {Humans ; *Melanoma/drug therapy/genetics/metabolism/pathology ; *Vemurafenib/pharmacology/therapeutic use ; *GTP Phosphohydrolases/genetics/metabolism ; *Mitochondria/metabolism/drug effects ; *Membrane Proteins/genetics/metabolism ; Cell Line, Tumor ; *Mutation ; *MAP Kinase Signaling System/drug effects ; Mitochondrial Dynamics/drug effects ; Antineoplastic Agents/pharmacology/therapeutic use ; Drug Resistance, Neoplasm/genetics/drug effects ; Cell Proliferation/drug effects ; Dynamins ; },
abstract = {Vemurafenib is a BRAF (rapidly accelerated fibrosarcoma B-type)-targeted therapy used to treat patients with advanced, unresectable melanoma. It inhibits the MAPK (mitogen-activated protein kinase)/ERK (extracellular signal-regulated kinase) pathway and tumor proliferation in BRAF[V600E]-mutated melanoma cells. Resistance to vemurafenib has been reported in melanoma patients due to secondary NRAS (neuroblastoma RAS viral oncogene homolog) mutations, which lead to paradoxical MAPK pathway activation and tumor proliferation. However, the impact of this paradoxical activation on mitochondrial dynamics and function in NRAS-mutated melanoma is unclear. Here, we investigated the effects of vemurafenib on NRAS[Q61R]-mutated melanoma cells, focusing on mitochondrial dynamics and function. As expected, vemurafenib did not exhibit cytotoxicity in SK-MEL-147 NRAS[Q61R]-mutated melanoma cells, even after 72 h of incubation. However, it significantly enhanced the MAPK/ERK signaling through paradoxical activation, accompanied by decreased expression of mitochondrial fusion proteins and activation of the fission protein DRP1 (dynamin-related protein 1), leading to small, rounded mitochondrial morphology. These observations were corroborated by transcriptome data obtained from NRAS-mutated melanoma patients, showing MFN1 (mitofusin 1) and OPA1 (optic atrophy 1) downregulation and DNM1L (DRP1 gene) upregulation. Interestingly, inhibition of mitochondrial fission with mdivi-1 or modulation of oxidative phosphorylation via respiratory chain inhibition or uncoupling significantly sensitized NRAS[Q61R]-mutated melanoma cells to vemurafenib. Despite vemurafenib's low cytotoxicity in NRAS-mutated melanoma, targeting mitochondrial dynamics and/or oxidative phosphorylation may offer a promising strategy for combined therapy.},
}

Humans
*Melanoma/drug therapy/genetics/metabolism/pathology
*Vemurafenib/pharmacology/therapeutic use
*GTP Phosphohydrolases/genetics/metabolism
*Mitochondria/metabolism/drug effects
*Membrane Proteins/genetics/metabolism
Cell Line, Tumor
*Mutation
*MAP Kinase Signaling System/drug effects
Mitochondrial Dynamics/drug effects
Antineoplastic Agents/pharmacology/therapeutic use
Drug Resistance, Neoplasm/genetics/drug effects
Cell Proliferation/drug effects
Dynamins

@article {pmid39950816,
year = {2025},
author = {Guo, B and Guo, G and Qi, W and Aizezi, M and Wu, C and Tian, M and Casulli, A and Zhang, W and Li, J},
title = {The genetic variation of mitochondrial sequences and pathological differences of Echinococcus multilocularis strains from different continents.},
journal = {Microbiology spectrum},
volume = {13},
number = {4},
pages = {e0131824},
pmid = {39950816},
issn = {2165-0497},
support = {2023TSYCTD0017//Tianshan talent training program/ ; 32072886,U1803282//MOST | National Natural Science Foundation of China (NSFC)/ ; 81830066//MOST | National Natural Science Foundation of China (NSFC)/ ; SKLHIDCA-2022-BC4//State Key Laboratory/ ; },
mesh = {Animals ; *Echinococcus multilocularis/genetics/classification ; Mice ; *Genetic Variation ; *Phylogeny ; *Echinococcosis/parasitology/pathology ; Mitochondria/genetics ; DNA, Mitochondrial/genetics ; Japan ; Humans ; },
abstract = {Alveolar echinococcosis is a lethal zoonotic disease caused by the fox tapeworm Echinococcus multilocularis. The parasite is widely distributed in the Northern Hemisphere and exhibits low genetic diversity among populations. To compare the differences among four E. multilocularis strains from different geographical locations, namely, Alaska (EM-AK), Japan (EM-JP), Xinjiang (EM-XJ), and Ningxia (EM-NX), their complete mitochondrial (mt) sequences were compared, and their induced pathological lesions were analyzed in mouse models. The complete mt sequence of EM-AK resulted in 0.84%-0.86% variation as compared with the other strains, which had a lower variation. Phylogenetic analysis and parsimony network indicated that EM-AK resulted in 30,000 years of evolutionary distance from the other three strains. EM-AK induced more pathological damage than the other three strains, which was likely to induce more host cell infiltration and acute granuloma in the liver. More importantly, EM-AK produced more protoscoleces than the other three strains, which may impact the transmission dynamics of the parasite. Given the geographical location of four strains, which is far from each other, and also the pathological differences, the strains of E. multilocularis are likely models for addressing the relationship and interfacial immune response between the host and the helminth.IMPORTANCEEchinococcus multilocularis is the causative agent of alveolar echinococcosis, which is considered the most serious parasitic disease in the Northern Hemisphere. There are many genotypes, but the pathogenic and mitochondria sequence and differences are still unclear. Therefore, this study showed both pathological and genetic differences between the four strains of E. multilocularis. EM-AK induced more severe immune responses and especially induced more host cell infiltration, which resulted in more severe granuloma in the liver. EM-JP has metacestode lesions morphologically closer to those of E. granulosus with clear cyst fluid. However, this strain produced much fewer protoscoleces (PSCs). Genetically, EM-AK is more distant from other strains.},
}

Animals
*Echinococcus multilocularis/genetics/classification
Mice
*Genetic Variation
*Phylogeny
*Echinococcosis/parasitology/pathology
Mitochondria/genetics
DNA, Mitochondrial/genetics
Japan
Humans

@article {pmid40128668,
year = {2025},
author = {Song, S and Cao, J and Xiang, H and Liu, Z and Jiang, W},
title = {Comparative mitogenomic analysis of Chinese cavefish Triplophysa (Cypriniformes: Nemacheilidae): novel gene tandem duplication and evolutionary implications.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {293},
pmid = {40128668},
issn = {1471-2164},
support = {32060128//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Cypriniformes/genetics ; *Genome, Mitochondrial ; *Evolution, Molecular ; *Gene Duplication ; *Phylogeny ; RNA, Transfer/genetics ; },
abstract = {BACKGROUND: Cavefish exhibit significant morphological changes that result in trade-offs in metabolic requirements and energy utilization in perpetual darkness. As cellular "powerhouses", mitochondria play crucial roles in energy metabolism, suggesting that mitochondrial genes have likely experienced selective pressures during cavefish evolution.

RESULTS: This study presents the first assembly of the complete mitogenome of Triplophysa yangi, a typical cavefish species in China. The mitogenome is 17,068 bp long, marking the longest recorded for the genus Triplophysa, and includes 13 protein-coding genes (PCGs), 2 rRNAs, 25 tRNAs, and a noncoding control region. An ~ 500 bp insertion between ND2 and WANCY regions was observed, comprising a large intact tandem repeat unit (A'-N'-OL'-C') flanked by two unannotated sequences (U1/U2). The evolutionary origin of this repeat unit may involve either in situ duplication events with subsequent functional divergence-where neofunctionalization, subfunctionalization, or pseudogenization drove differential mutation rates between paralogs-or alternatively, horizontal acquisition from exogenous genetic material that became functionally integrated into the ancestral T. yangi mitogenome through co-option mechanisms. Phylogenetic analyses revealed two major clades within Triplophysa-epigean and hypogean lineages-consistent with previous classifications, while cave-restricted species exhibited signs of parallel evolution within the hypogean lineage. Selective pressure analysis indicated that the hypogean lineage (cave-dwelling groups, II & III) have a significantly increased ratio of nonsynonymous to synonymous substitution rates (ω) compared to the epigean lineage (surface-dwelling group, I), suggesting a combination of adaptive selection and relaxed functional constraints in cave-dwelling species.

CONCLUSIONS: The duplication of tRNAs in T. yangi and the potential positive selection sites identified in Triplophysa cavefish further indicated adaptive evolution in mitochondrial PCGs in response to extreme subterranean conditions.},
}

Animals
*Cypriniformes/genetics
*Genome, Mitochondrial
*Evolution, Molecular
*Gene Duplication
*Phylogeny
RNA, Transfer/genetics

@article {pmid40127832,
year = {2025},
author = {Liu, Q and Mao, W and Wang, Y and Xiao, J and Saha, S and Gao, T and Liu, F},
title = {Whole genome sequencing and phylogenetic analyses of the Sillaginidae family fish.},
journal = {Molecular phylogenetics and evolution},
volume = {},
number = {},
pages = {108340},
doi = {10.1016/j.ympev.2025.108340},
pmid = {40127832},
issn = {1095-9513},
abstract = {For a long time, the taxonomic study of the Sillaginidae family of fish has been relatively slow, leaving the evolutionary relationships among species unclear. Previous research has mainly relied on morphological characteristics, with molecular studies limited primarily to mitochondrial genomics, including analyses of gene fragments and whole mitochondrial genomic sequence. This approach resulted in less precise and comprehensive species identification. In this study, we employed high-depth whole-genome sequencing (WGS) and genome surveys on 13 specimens representing 9 species of Sillaginidae fish collected from the wild. Our analysis included a thorough genomic survey and the assembly of draft genomes for each specimen. The genome sizes of Sillaginidae species are highly similar, ranging from 511.71 Mb to 578.27 Mb, with most individuals exhibiting repeat sequences content below 34.69 %. After the genome draft assembly of each sample, we identified conserved genes and shared consistent sequences among individuals and constructed a species phylogenetic tree based on these data. The results revealed that Sillago ingenua occupies the basal branch, followed by S. maculata and S. aeolus, then Sillaginopsis panijus, S. japonica and S. asiatica, and finally S. nigrofasciata and S. cf. sihama. Subsequently, we validated the phylogenetic tree using genome-wide single nucleotide variations, and the results were highly consistent. This research provides, for the first time, a whole-genome perspective on the evolutionary relationships among Sillaginidae species, offering valuable insights into their taxonomy and historical evolution.},
}

@article {pmid40123256,
year = {2025},
author = {Richmond, JQ and Gottscho, AD and Jockusch, EL and Leaché, AD and Fisher, RN and Reeder, TW},
title = {Genomic discordance throws a wrench in the parallel speciation hypothesis for scincid lizards.},
journal = {Evolution; international journal of organic evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/evolut/qpaf059},
pmid = {40123256},
issn = {1558-5646},
abstract = {Parallel evolution of the same reproductive isolation barrier within a taxon is an indicator of ecology's role in speciation (i.e., parallel speciation), yet spatiotemporal variability in the efficacy of the barrier can present challenges to retracing how it evolved. Here, we revisit the evidence for a candidate example of parallel speciation in a clade of scincid lizards (the Plestiodon skiltonianus complex) using genomic data, with emphasis on determining whether hybridization may have confounded the phylogenetic signals of parallelism for this group. Our results show a striking case of genealogical discordance, where mitochondrial loci support multiple origins of a derived large-bodied morphotype (Plestiodon gilberti) within a small-bodied ancestor (Plestiodon skiltonianus), while nuclear loci indicate a single origin. We attribute the discordance to separate, temporally-spaced hybridization events that led to asymmetric capture of P. skiltonianus mitochondria in different regional lineages of P. gilberti. Nuclear introgression showed a similar directional bias but was less pervasive. We demonstrate how a mechanical reproductive barrier previously identified for this group explains the asymmetry of mitochondrial introgression, given that hybrid matings are most likely when the male is P. gilberti and the female is P. skiltonianus. We then use permutation tests of morphological data to provide evidence that the mechanical barrier is less stringent in areas where hybridization is inferred to have occurred. Our results demonstrate how biased hybridization can dictate which genetic variants are transmitted between species and emphasize the importance of accounting for introgression and deep coalescence in identifying phyletic signatures of parallel speciation.},
}

@article {pmid40114504,
year = {2025},
author = {Iverson, ENK and Criswell, A and Havird, JC},
title = {Stronger evidence for relaxed selection than adaptive evolution in high-elevation animal mtDNA.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msaf061},
pmid = {40114504},
issn = {1537-1719},
abstract = {Mitochondrial (mt) genes are the subject of many adaptive hypotheses due to the key role of mitochondria in energy production and metabolism. One widespread adaptive hypothesis is that selection imposed by life at high elevation leads to the rapid fixation of beneficial alleles in mtDNA, reflected in the increased rates of mtDNA evolution documented in many high-elevation species. However, the assumption that fast mtDNA evolution is caused by positive, rather than relaxed purifying selection has rarely been tested. Here, we calculated the dN/dS ratio, a metric of nonsynonymous substitution bias, and explicitly tested for relaxed selection in the mtDNA of over 700 species of terrestrial vertebrates, freshwater fishes, and arthropods, with information on elevation and latitudinal range limits, range sizes, and body sizes. We confirmed that mitochondrial genomes of high-elevation taxa have slightly higher dN/dS ratios compared to low-elevation relatives. High-elevation species tend to have smaller ranges, which predict higher dN/dS ratios and more relaxed selection across species and clades, while absolute elevation and latitude do not predict higher dN/dS. We also find a positive relationship between body mass and dN/dS, supporting a role for small effective population size leading to relaxed selection. We conclude that higher mt dN/dS among high-elevation species is more likely to reflect relaxed selection due to smaller ranges and reduced effective population size than adaptation to the environment. Our results highlight the importance of rigorously testing adaptive stories against non-adaptive alternative hypotheses, especially in mt genomes.},
}

@article {pmid40112915,
year = {2025},
author = {Park, YJ and Pang, WK and Ryu, DY and Rahman, MS and Pang, MG},
title = {Spatiotemporal translation of sperm acrosome associated proteins during early capacitation modulates sperm fertilizing ability.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2025.03.035},
pmid = {40112915},
issn = {2090-1224},
abstract = {INTRODUCTION: Despite the lack of essential cytoplasmic organelles in mature spermatozoa, which creates unfavorable conditions for transcription and translation, the presence of various mRNA and proteins during capacitation suggests potential for de novo protein synthesis.

OBJECTIVES: We applied a metabolic labeling method using a fluorescent noncanonical amino acid tagging system (FUNCAT) and proximity ligation method (PLA) in normal and reduced fertility spermatozoa to detect different translation phenomena during sperm capacitation according to their fertility.

METHODS: We explored different proteome changes in spermatozoa according to the time-sequential capacitation process (0, 20, 40, 60, and 120 min) between normal [average fertility rate (FR) = 77.44 % ± 1.51] and reduced fertility (average FR = 58.57 % ± 1.64) spermatozoa bull spermatozoa, as the representative male fertility models owing to their broad spectrum of fertility phenotypes. Moreover, the FUNCAT/PLA method was used to detect and visualize different translation phenomena during sperm capacitation according to fertility.

RESULTS: We found that sperm-associated protein (SPACA) 1 and SPACA5 were newly synthesized in the head of normal-fertility spermatozoa, whereas a lack of newly synthesized proteins in the head and a relatively earlier loss of SPACA1 and SPACA5 were observed in the reduced-fertility spermatozoa. Moreover, the mitochondrial translation inhibitor, chloramphenicol, partially inhibited sperm translation and delayed translocation, suggesting that mitochondria participate in sperm translation.

CONCLUSION: Our results unveil time-sequential microenvironmental changes in sperm proteomes during capacitation, which lead to the orchestra of proteins that complete fertilization. Fertile spermatozoa are selected through inter-competition during the journey of fertilization in the female reproductive tract. This study provides an overview of how translation dynamics acts on the sperm selection and influence the evolution of sperm fertility.},
}

@article {pmid40107722,
year = {2025},
author = {Dondi, A and Borgsmüller, N and Ferreira, PF and Haas, BJ and Jacob, F and Heinzelmann-Schwarz, V and , and Beerenwinkel, N},
title = {De novo detection of somatic variants in high-quality long-read single-cell RNA sequencing data.},
journal = {Genome research},
volume = {},
number = {},
pages = {},
doi = {10.1101/gr.279281.124},
pmid = {40107722},
issn = {1549-5469},
abstract = {In cancer, genetic and transcriptomic variations generate clonal heterogeneity, leading to treatment resistance. Long-read single-cell RNA sequencing (LR scRNA-seq) has the potential to detect genetic and transcriptomic variations simultaneously. Here, we present LongSom, a computational workflow leveraging high-quality LR scRNA-seq data to call de novo somatic single-nucleotide variants (SNVs), including in mitochondria (mtSNVs), copy number alterations (CNAs), and gene fusions, to reconstruct the tumor clonal heterogeneity. Before somatic variant calling, LongSom reannotates marker gene-based cell types using cell mutational profiles. LongSom distinguishes somatic SNVs from noise and germline polymorphisms by applying an extensive set of hard filters and statistical tests. Applying LongSom to human ovarian cancer samples, we detected clinically relevant somatic SNVs that were validated against matched DNA samples. Leveraging somatic SNVs and fusions, LongSom found subclones with different predicted treatment outcomes. In summary, LongSom enables de novo variant detection without the need for normal samples, facilitating the study of cancer evolution, clonal heterogeneity, and treatment resistance.},
}

@article {pmid40107618,
year = {2025},
author = {Thalhofer, V and Doktor, C and Philipp, L and Betat, H and Mörl, M},
title = {An alternative adaptation strategy of the CCA-adding enzyme to accept non-canonical tRNA substrates in Ascaris suum.},
journal = {The Journal of biological chemistry},
volume = {},
number = {},
pages = {108414},
doi = {10.1016/j.jbc.2025.108414},
pmid = {40107618},
issn = {1083-351X},
abstract = {Playing a central role in translation, tRNAs act as an essential adapter linking the correct amino acid to the corresponding mRNA codon in translation. Due to this function, all tRNAs exhibit a typical secondary and tertiary structure to be recognized by the tRNA maturation enzymes as well as many components of the translation machinery. Yet, there is growing evidence for structurally deviating tRNAs in metazoan mitochondria, requiring a co-evolution and adaptation of these enzymes to the unusual structures of their substrates. Here, it is shown that the CCA-adding enzyme of Ascaris suum carries such a specific adaptation in form of a C-terminal extension. The corresponding enzymes of other nematodes also carry such extensions, and many of them have an additional adaptation in a small region of their N-terminal catalytic core. Thus, the presented data indicates that these enzymes evolved two distinct strategies to tolerate non-canonical tRNAs as substrates for CCA-incorporation. The identified C-terminal extension represents a surprising case of convergent evolution in tRNA substrate adaptation, as the nematode mitochondrial translation factor EF-Tu1 carries a similar extension that is essential for efficient binding to such structurally deviating tRNAs.},
}

@article {pmid40090735,
year = {2025},
author = {Yabuki, A and Fujii, C and Yazaki, E and Tame, A and Mizuno, K and Obayashi, Y and Takao, Y},
title = {Massive RNA Editing in Ascetosporean Mitochondria.},
journal = {Microbes and environments},
volume = {40},
number = {1},
pages = {},
doi = {10.1264/jsme2.ME24070},
pmid = {40090735},
issn = {1347-4405},
mesh = {*RNA Editing ; *Mitochondria/genetics ; *Genome, Mitochondrial/genetics ; High-Throughput Nucleotide Sequencing ; Eukaryota/genetics/classification ; Phylogeny ; Adenosine Deaminase/genetics/metabolism ; },
abstract = {Ascetosporeans are parasitic protists of invertebrates. A deep sequencing ana-lysis of species within the orders Mikrocytida, Paramyxida, and Haplosporida using metagenomic approaches revealed that their mitochondria were functionally reduced and their organellar genomes were lacking. Ascetosporeans belonging to the order Paradinida have not been sequenced, and the nature of their mitochondria remains unclear. We herein established two cultures of Paradinida and conducted DNA and RNA sequencing ana-lyses. The results obtained indicate that mitochondrial function in paradinids was not reduced and their organellar genomes were retained. In contrast, their mitochondrial genomes were involved in massive A-to-I and C-to-U substitution types of RNA editing. All edits in protein-coding genes were nonsynonymous substitutions, and likely had a restorative function against negative mutations. Furthermore, we detected possible sequences of DYW type of pentatricopeptide repeat (PPR-DYW) protein and a homologue of adenosine deaminase acting on RNA (ADAR-like), which are key enzymes for C-to-U and A-to-I substitutions, respectively. An immunofluorescence ana-lysis showed that ADAR-like of paradinids may specifically localize within mitochondria. These results expand our knowledge of the diversity and complexity of organellar RNA editing phenomena.},
}

*RNA Editing
*Mitochondria/genetics
*Genome, Mitochondrial/genetics
High-Throughput Nucleotide Sequencing
Eukaryota/genetics/classification
Phylogeny
Adenosine Deaminase/genetics/metabolism

@article {pmid40081380,
year = {2025},
author = {Morel, CA and Asencio, C and Moreira, D and Blancard, C and Salin, B and Gontier, E and Duvezin-Caubet, S and Rojo, M and Bringaud, F and Tetaud, E},
title = {A new member of the dynamin superfamily modulates mitochondrial membrane branching in Trypanosoma brucei.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2025.02.033},
pmid = {40081380},
issn = {1879-0445},
abstract = {Unlike most other eukaryotes, where mitochondria continuously fuse and divide, the mitochondrion of trypanosome cells forms a single and continuously interconnected network that divides only during cytokinesis. However, the machinery governing mitochondrial remodeling and interconnection of trypanosome mitochondrion remain largely unknown. We functionally characterize a new member of the dynamin superfamily protein (DSP) from T. brucei (TbMfnL), which shares similarity with a family of homologs present in various eukaryotic and prokaryotic phyla but not in opisthokonts like mammals and budding yeast. The sequence and domain organization of TbMfnL is distinct, and it is phylogenetically very distant from the yeast and mammalian dynamin-related proteins involved in mitochondrial fusion/fission dynamics, such as optic atrophy 1 (Opa1) and mitofusin (Mfn). TbMfnL localizes to the inner mitochondrial membrane facing the matrix and, upon overexpression, induces a strong increase in the interconnection and branching of mitochondrial filaments in a GTPase-dependent manner. TbMfnL is a component of a novel membrane remodeling machinery with an unprecedented matrix-side localization that is able to modulate the degree of inter-mitochondrial connections.},
}

@article {pmid40037840,
year = {2025},
author = {Medini, H and Mishmar, D},
title = {Vertebrates show coordinated elevated expression of mitochondrial and nuclear genes after birth.},
journal = {Genome research},
volume = {35},
number = {3},
pages = {459-474},
doi = {10.1101/gr.279700.124},
pmid = {40037840},
issn = {1549-5469},
mesh = {Animals ; *Gene Expression Regulation, Developmental ; Vertebrates/genetics ; Cell Nucleus/metabolism/genetics ; Mitochondria/genetics/metabolism ; Genes, Mitochondrial ; Humans ; Oxidative Phosphorylation ; Chickens/genetics ; },
abstract = {Interactions between mitochondrial and nuclear factors are essential to life. Nevertheless, the importance of coordinated regulation of mitochondrial-nuclear gene expression (CMNGE) to changing physiological conditions is poorly understood and is limited to certain tissues and organisms. We hypothesized that CMNGE is important for development across vertebrates and, hence, should be conserved. As a first step, we analyzed more than 1400 RNA-seq experiments performed during prenatal development, in neonates, and in adults across vertebrate evolution. We find conserved sharp elevation of CMNGE after birth, including oxidative phosphorylation (OXPHOS) and mitochondrial ribosome genes, in the heart, hindbrain, forebrain, and kidney across mammals, as well as in Gallus gallus and in the lizard Anolis carolinensis This is accompanied by elevated expression of TCA cycle enzymes and reduction in hypoxia response genes, suggesting a conserved cross-tissue metabolic switch after birth/hatching. Analysis of about 70 known regulators of mitochondrial gene expression reveals consistently elevated expression of PPARGC1A (also known as Pgc-1alpha) and CEBPB after birth/hatching across organisms and tissues, thus highlighting them as candidate regulators of CMNGE upon transition to the neonate. Analyses of Danio rerio, Xenopus tropicalis, Caenorhabditis elegans, and Drosophila melanogaster reveal elevated CMNGE prior to hatching in X. tropicalis and in D. melanogaster, which is associated with the emergence of muscle activity. Lack of such an ancient pattern in mammals and in chickens suggests that it was lost during radiation of terrestrial vertebrates. Taken together, our results suggest that regulated CMNGE after birth reflects an essential metabolic switch that is under strong selective constraints.},
}

Animals
*Gene Expression Regulation, Developmental
Vertebrates/genetics
Cell Nucleus/metabolism/genetics
Mitochondria/genetics/metabolism
Genes, Mitochondrial
Humans
Oxidative Phosphorylation
Chickens/genetics

@article {pmid39893979,
year = {2025},
author = {Duan, C and Zhao, Y and Xiao, Y and Hou, Y and Gong, W and Zhang, H and Wang, Y and Nie, X},
title = {Lithium with environmentally relevant concentrations interferes with mitochondrial function, antioxidant response, and autophagy processes in Daphnia magna, leading to changes in life-history traits and behavior.},
journal = {Journal of hazardous materials},
volume = {488},
number = {},
pages = {137420},
doi = {10.1016/j.jhazmat.2025.137420},
pmid = {39893979},
issn = {1873-3336},
mesh = {Animals ; *Daphnia/drug effects ; *Autophagy/drug effects ; *Water Pollutants, Chemical/toxicity ; *Mitochondria/drug effects ; *Lithium/toxicity ; Oxidative Stress/drug effects ; Antioxidants/metabolism ; Life History Traits ; Behavior, Animal/drug effects ; Reactive Oxygen Species/metabolism ; Female ; Daphnia magna ; },
abstract = {With the increasing production and use of lithium-based products, concerns over lithium pollution in aquatic ecosystems are increasing, whereas research on its toxicity mechanisms in aquatic organisms remains limited. The main objective of the present study was to explore the effects of environmentally relevant concentrations of lithium exposure on the life-history strategy, behavior, antioxidant system, and autophagy process of Daphnia magna. Acute (24-96 h) and chronic (21 days) exposure experiments under three lithium treatments (low: 8.34 μg/L, medium: 83.44 μg/L, and high: 834.41 μg/L) were conducted. The results indicated that exposure to medium and high lithium concentrations led to eye and tail deformities in D. magna. Furthermore, developmental and reproductive parameters such as body length, total neonates per female, and average neonates per time were negatively influenced. Lithium also interfered with energy metabolism to cause the decreasing swimming speed and the reduction in the swimming range. In addition, lithium exposure affected the expression of gsk-3β, further disrupting the dynamic balance of mitochondrial fission, fusion, and regeneration, which caused ROS accumulation and induced oxidative stress. D. magna attenuated the stress by activating the FoxO/SESN and Nrf2/Keap1 pathways, synergistically enhancing downstream antioxidant enzymes expression. Concurrently, D. magna also mitigated oxidative stress and mitochondrial damage by promoting autophagy and inhibiting apoptosis. In summary, lithium harmed the physiological and biochemical functions of D. magna through multiple mechanisms, suggesting that environmental lithium pollution may pose a potential threat to aquatic organisms.},
}

Animals
*Daphnia/drug effects
*Autophagy/drug effects
*Water Pollutants, Chemical/toxicity
*Mitochondria/drug effects
*Lithium/toxicity
Oxidative Stress/drug effects
Antioxidants/metabolism
Life History Traits
Behavior, Animal/drug effects
Reactive Oxygen Species/metabolism
Female
Daphnia magna

@article {pmid40076588,
year = {2025},
author = {Zhou, W and Cao, X and Li, H and Cui, X and Diao, X and Qiao, Z},
title = {Genomic Analysis of Hexokinase Genes in Foxtail Millet (Setaria italica): Haplotypes and Expression Patterns Under Abiotic Stresses.},
journal = {International journal of molecular sciences},
volume = {26},
number = {5},
pages = {},
pmid = {40076588},
issn = {1422-0067},
mesh = {*Setaria Plant/genetics ; *Stress, Physiological/genetics ; *Gene Expression Regulation, Plant ; *Phylogeny ; *Hexokinase/genetics/metabolism ; *Haplotypes ; Plant Proteins/genetics/metabolism ; Evolution, Molecular ; },
abstract = {Hexokinases (HXKs) in plants are multifunctional enzymes that not only phosphorylate hexose but also function as glucose sensors, integrating nutrient, light, and hormone signaling networks to regulate cell metabolism and signaling pathways, thereby controlling growth and development in response to environmental changes. To date, limited information is available regarding the HXKs of foxtail millet (Setaria italica L.). In this study, six HXK genes were identified and characterized in foxtail millet. Phylogenetic analysis revealed that the foxtail millet hexokinases were classified into three subfamilies, corresponding to the two types (B-type and C-type) of hexokinases in plants. Gene structure and conserved motif analysis showed that the SiHXKs exhibited varying numbers of introns and exons, with proteins in each subfamily showing similar motif organization. Evolutionary divergence analysis indicated that the foxtail millet HXK and green foxtail HXK genes families underwent both positive and negative selection and experienced a large-scale duplication event approximately 1.18-154.84 million years ago. Expression analysis revealed that these genes are widely expressed in roots, stems, leaves, panicles, anthers, and seeds, with most genes showing significantly increased expression in roots under abiotic stress conditions, including 20% PEG 6000 (drought stress), 200 μmol/L NaCl (salt stress), and 1 μmol/L BR (brassinosteroid-mediated stress response). These results suggest that these genes may play a pivotal role in enhancing stress tolerance. Subcellular localization assay showed that SiHXK5 and SiHXK6 were predominantly localized in mitochondria. Haplotype analysis revealed that SiHXK3-H1 was associated with higher plant height and grain yield. These findings provide valuable insights into the functional characteristics of HXK genes, especially in the context of marker-assisted selection and the pyramiding of advantageous haplotypes in foxtail millet breeding programs.},
}

*Setaria Plant/genetics
*Stress, Physiological/genetics
*Gene Expression Regulation, Plant
*Phylogeny
*Hexokinase/genetics/metabolism
*Haplotypes
Plant Proteins/genetics/metabolism
Evolution, Molecular

@article {pmid40075306,
year = {2025},
author = {Zhou, N and Wang, X and Xia, Y and Liu, Z and Luo, L and Jin, R and Tong, X and Shi, Z and Wang, Z and Sui, H and Ma, Y and Li, Y and Cao, Z and Zhang, Y},
title = {Comparatively profiling the transcriptome of human, Porcine and mouse oocytes undergoing meiotic maturation.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {236},
pmid = {40075306},
issn = {1471-2164},
support = {2020LCX015//Anhui Province Innovation and Entrepreneurship Support Program for Returnee Scholar/ ; 2021YFA0805905//Sub-project of National Key Research and Development Program of China/ ; AHCYJSTX-04//Special Fund for Anhui Agriculture Research System/ ; },
mesh = {Animals ; *Oocytes/metabolism ; Mice ; *Meiosis/genetics ; Humans ; Swine ; *Gene Expression Profiling ; *Transcriptome ; Female ; Oogenesis/genetics ; Species Specificity ; },
abstract = {BACKGROUND: Oocyte maturation is a critical process responsible for supporting preimplantation embryo development and full development to term. Understanding oocyte gene expression is relevant given the unique molecular mechanism present in this gamete. Comparative transcriptome analysis across species offers a powerful approach to uncover conserved and species-specific genes involved in the molecular regulation of oocyte maturation throughout evolution.

RESULTS: Transcriptome analysis identified 4,625, 3,824, 4,972 differentially expressed genes (DEGs) between the germinal vesicle (GV) and metaphase II (MII) stage in human, porcine and mouse oocytes respectively. These DEGs showed dynamic changes associated with oocyte maturation. Functional enrichment analysis revealed that the DEGs in all three species were mainly involved in DNA replication, cell cycle and redox regulation. Comparative transcriptome analysis identified 551 conserved DEGs in the three species with significant enrichment in mitochondria and mitochondrial intima.

CONCLUSIONS: This study provides a systematic comparative analysis of oocyte meiotic maturation in humans, pigs and mice identifying both conserved and species-specific patterns during oocyte meiosis. Our findings also implied that the selection of oocyte expressed genes among these three species could form a basis for further exploring their functional roles in human oocyte maturation.},
}

Animals
*Oocytes/metabolism
Mice
*Meiosis/genetics
Humans
Swine
*Gene Expression Profiling
*Transcriptome
Female
Oogenesis/genetics
Species Specificity

@article {pmid40043709,
year = {2025},
author = {Ping, J and Liu, X and Lu, Y and Quan, C and Fan, P and Lu, H and Li, Q and Wang, C and Zhang, Z and Liu, M and Chen, S and Chang, L and Jiang, Y and Huang, Q and Liu, J and Wuren, T and Liu, H and Hao, Y and Kang, L and Liu, G and Lu, H and Wei, X and Wang, Y and Li, Y and Guo, H and Cui, Y and Zhang, H and Zhang, Y and Zhai, Y and He, Y and Zheng, W and Qi, X and Ouzhuluobu, and Ma, H and Yang, L and Wang, X and Jin, W and Cui, Y and Ge, R and Wu, S and Wei, Y and Su, B and He, F and Zhang, H and Zhou, G},
title = {A highland-adaptation variant near MCUR1 reduces its transcription and attenuates erythrogenesis in Tibetans.},
journal = {Cell genomics},
volume = {5},
number = {3},
pages = {100782},
doi = {10.1016/j.xgen.2025.100782},
pmid = {40043709},
issn = {2666-979X},
mesh = {Humans ; *Erythropoiesis/genetics ; Tibet ; *Calcium/metabolism ; Calcium-Calmodulin-Dependent Protein Kinase Kinase/genetics/metabolism ; Quantitative Trait Loci ; Mitochondria/metabolism/genetics ; Male ; Altitude ; TOR Serine-Threonine Kinases/metabolism/genetics ; Adaptation, Physiological/genetics ; Transcription, Genetic/genetics ; Female ; Adult ; Calcium Channels/genetics/metabolism ; Polymorphism, Single Nucleotide ; East Asian People ; },
abstract = {To identify genomic regions subject to positive selection that might contain genes involved in high-altitude adaptation (HAA), we performed a genome-wide scan by whole-genome sequencing of Tibetan highlanders and Han lowlanders. We revealed a collection of candidate genes located in 30 genomic loci under positive selection. Among them, MCUR1 at 6p23 was a novel pronounced candidate. By single-cell RNA sequencing and comprehensive functional studies, we demonstrated that MCUR1 depletion leads to impairment of erythropoiesis under hypoxia and normoxia. Mechanistically, MCUR1 knockdown reduced mitochondrial Ca[2+] uptake and then concomitantly increased cytosolic Ca[2+] levels, which thereby reduced erythropoiesis via the CAMKK2-AMPK-mTOR axis. Further, we revealed rs61644582 at 6p23 as an expression quantitative trait locus for MCUR1 and a functional variant that confers an allele-specific transcriptional regulation of MCUR1. Overall, MCUR1-mediated mitochondrial Ca[2+] homeostasis is highlighted as a novel regulator of erythropoiesis, deepening our understanding of the genetic mechanism of HAA.},
}

Humans
*Erythropoiesis/genetics
Tibet
*Calcium/metabolism
Calcium-Calmodulin-Dependent Protein Kinase Kinase/genetics/metabolism
Quantitative Trait Loci
Mitochondria/metabolism/genetics
Male
Altitude
TOR Serine-Threonine Kinases/metabolism/genetics
Adaptation, Physiological/genetics
Transcription, Genetic/genetics
Female
Adult
Calcium Channels/genetics/metabolism
Polymorphism, Single Nucleotide
East Asian People

@article {pmid40072502,
year = {2025},
author = {Kemph, A and Kharel, K and Tindell, SJ and Arkov, AL and Lynch, JA},
title = {Novel structure and composition of the unusually large germline determinant of the wasp Nasonia vitripennis.},
journal = {Molecular biology of the cell},
volume = {},
number = {},
pages = {mbcE24110499},
doi = {10.1091/mbc.E24-11-0499},
pmid = {40072502},
issn = {1939-4586},
abstract = {Specialized, maternally derived ribonucleoprotein (RNP) granules play an important role in specifying the primordial germ cells in many animal species. Typically, these germ granules are small (∼100 nm to a few microns in diameter) and numerous; in contrast, a single, extremely large granule called the oosome plays the role of germline determinant in the wasp Nasonia vitripennis. The organizational basis underlying the form and function of this unusually large membraneless RNP granule remains an open question. Here we use a combination of super-resolution and transmission electron microscopy to investigate the composition and morphology of the oosome. We show evidence which suggests the oosome has properties of a viscous liquid or elastic solid. The most prominent feature of the oosome is a branching mesh-like network of high abundance mRNAs that pervades the entire structure. Homologs of the core germ granule proteins Vasa and Oskar do not appear to nucleate this network but rather are distributed adjacently as separate puncta. Low abundance RNAs appear to cluster in puncta that similarly do not overlap with the protein puncta. Several membrane-bound organelles, including lipid droplets and rough ER-like vesicles, are incorporated within the oosome, whereas mitochondria are nearly entirely excluded. Our findings show that the remarkably large size of the oosome is reflected in a complex sub-granular organization and suggest that the oosome is a powerful model for probing interactions between membraneless and membrane-bound organelles, structural features that contribute to granule size, and the evolution of germ plasm in insects. [Media: see text] [Media: see text].},
}

@article {pmid40056111,
year = {2025},
author = {Sun, A and Wang, WX},
title = {Photodegradation Controls of Potential Toxicity of Secondary Sunscreen-Derived Microplastics and Associated Leachates.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c12077},
pmid = {40056111},
issn = {1520-5851},
abstract = {The escalating environmental concern over secondary microplastics (SMPs) stems from their physicochemical evolution from primary microplastics (PMPs), yet the contribution of varying physicochemical transformations to the ultimate environmental risks remains unknown. In this study, a photomechanical degradation process was employed to convert the primary sunscreen-derived microplastics (SDMPs) into secondary SDMPs. While mechanical degradation caused physical fragmentation, photodegradation induced both physical and chemical alterations, introducing surface oxidation, chemical bond scission, and cross-linking to the secondary SDMPs. Employing a combination of alkaline digestion and pyrolysis GC-MS techniques, it was observed that both physical fragmentation and photooxidation led to heightened intracellular sequestration of MPs. Although the bioaccumulated SDMPs could be indicated by the enlarged lysosomes and fragmented mitochondria, toxicity of secondary SDMPs at the cellular level was primarily driven by chemical transformations post-photodegradation. A nontargeted analysis employing high-resolution mass spectrometry identified 46 plastic-associated compounds in the leachate, with photodegradation-induced chemical transformations playing a crucial role in the dissociation of hydrophobic additives and oxidative conversion of leached compounds. The toxicity of the leachate was exacerbated by photodegradation, with mitochondrial fragmentation serving as the primary subcellular biomarker, indicative of leachate toxicity. This study elucidates the pivotal role of photodegradation in augmenting the cytotoxicity of secondary SDMPs, shedding light on the intricate interplay between physicochemical transformations and environmental risks.},
}

@article {pmid40043708,
year = {2025},
author = {Thomas, HB and Demain, LAM and Cabrera-Orefice, A and Schrauwen, I and Shamseldin, HE and Rea, A and Bharadwaj, T and Smith, TB and Oláhová, M and Thompson, K and He, L and Kaur, N and Shukla, A and Abukhalid, M and Ansar, M and Rehman, S and Riazuddin, S and Abdulwahab, F and Smith, JM and Stark, Z and Mancilar, H and Tumer, S and Esen, FN and Uctepe, E and Topcu, V and Yesilyurt, A and Afzal, E and Salari, M and Carroll, C and Zifarelli, G and Bauer, P and Kor, D and Bulut, FD and Houlden, H and Maroofian, R and Carrera, S and Yue, WW and Munro, KJ and Alkuraya, FS and Jamieson, P and Ahmed, ZM and Leal, SM and Taylor, RW and Wittig, I and O'Keefe, RT and Newman, WG},
title = {Bi-allelic variants in MRPL49 cause variable clinical presentations, including sensorineural hearing loss, leukodystrophy, and ovarian insufficiency.},
journal = {American journal of human genetics},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajhg.2025.02.005},
pmid = {40043708},
issn = {1537-6605},
abstract = {Combined oxidative phosphorylation deficiency (COXPD) is a rare multisystem disorder that is clinically and genetically heterogeneous. Genome sequencing identified bi-allelic MRPL49 variants in individuals from nine unrelated families with presentations ranging from Perrault syndrome (primary ovarian insufficiency and sensorineural hearing loss) to severe childhood onset of leukodystrophy, learning disability, microcephaly, and retinal dystrophy. Complexome profiling of fibroblasts from affected individuals revealed reduced levels of the small mitochondrial ribosomal subunits and a more pronounced reduction of the large mitochondrial ribosomal subunits. There was no evidence of altered mitoribosomal assembly. The reductions in levels of oxidative phosphorylation (OXPHOS) enzyme complexes I and IV are consistent with a form of COXPD associated with bi-allelic MRPL49 variants, expanding the understanding of how disruption of the mitochondrial ribosomal large subunit results in multisystem phenotypes.},
}

@article {pmid40029892,
year = {2025},
author = {Paul, SK and Islam, MSU and Akter, N and Zohra, FT and Rashid, SB and Ahmed, MS and Rahman, SM and Sarkar, MAR},
title = {Genome-wide identification and characterization of FORMIN gene family in cotton (Gossypium hirsutum L.) and their expression profiles in response to multiple abiotic stress treatments.},
journal = {PloS one},
volume = {20},
number = {3},
pages = {e0319176},
pmid = {40029892},
issn = {1932-6203},
mesh = {*Gossypium/genetics ; *Stress, Physiological/genetics ; *Phylogeny ; *Gene Expression Regulation, Plant ; *Plant Proteins/genetics/metabolism ; *Multigene Family ; Formins/genetics/metabolism ; Genome, Plant ; Evolution, Molecular ; Genes, Plant ; },
abstract = {FORMIN proteins distinguished by FH2 domain, are conserved throughout evolution and widely distributed in eukaryotic organisms. These proteins interact with various signaling molecules and cytoskeletal proteins, playing crucial roles in both biotic and abiotic stress responses. However, the functions of FORMINs in cotton (Gossypium hirsutum L.) remain uncovered. In this study, 46 FORMIN genes in G. hirsutum (referred to as GhFH) were systematically identified. The gene structures, conserved domains, and motifs of these GhFH genes were thoroughly explored. Phylogenetic and structural analysis classified these 46 GhFH genes into five distinct groups. In silico subcellular localization, prediction suggested that GhFH genes are distributed across various cellular compartments, including the nucleus, extracellular space, cytoplasm, mitochondria, cytoskeleton, plasma membrane, endoplasmic reticulum, and chloroplasts. Evolutionary and functional diversification analyses, based on on-synonymous (Ka) and synonymous (Ks) ratios and gene duplication events, indicated that GhFH genes have evolved under purifying selection. The analysis of cis-acting elements suggested that GhFH genes may be involved in plant growth, hormone regulation, light response, and stress response. Results from transcriptional factors TFs and gene ontology analysis indicate that FORMIN proteins regulate cell wall structure and cytoskeleton dynamics by reacting to hormone signals associated with environmental stress. Additionally, 45 putative ghr-miRNAs were identified from 32 families targeting 33 GhFH genes. Expression analysis revealed that GhFH1, GhFH10, GhFH20, GhFH24, and GhFH30 exhibited the highest levels of expression under red, blue, and white light conditions. Further, GhFH9, GhFH20, and GhFH30 displayed higher expression levels under heat stress, while GhFH20 and GhFH30 showed increased expression under salt stress compared to controls. The result suggests that GhFH20 and GhFH30 genes could play significant roles in the development of G. hirsutum under heat and salt stresses. Overall these findings enhance our understanding of the biological functions of the cotton FORMIN family, offering prospects for developing stress-resistant cotton varieties through manipulation of GhFH gene expression.},
}

*Gossypium/genetics
*Stress, Physiological/genetics
*Phylogeny
*Gene Expression Regulation, Plant
*Plant Proteins/genetics/metabolism
*Multigene Family
Formins/genetics/metabolism
Genome, Plant
Evolution, Molecular
Genes, Plant

@article {pmid39993486,
year = {2025},
author = {He, M and Li, S and Sun, J and Lv, X and Li, Y and Song, L},
title = {CgVDAC2 participated in haemocyte mitophagy induced by Vibrio splendidus in the Pacific oyster Crassostrea gigas.},
journal = {Fish & shellfish immunology},
volume = {160},
number = {},
pages = {110226},
doi = {10.1016/j.fsi.2025.110226},
pmid = {39993486},
issn = {1095-9947},
mesh = {Animals ; *Vibrio/physiology ; *Crassostrea/immunology/genetics ; *Hemocytes/immunology ; *Mitophagy/immunology ; *Voltage-Dependent Anion Channel 2/genetics/immunology ; Immunity, Innate/genetics ; Gene Expression Regulation/immunology ; Phylogeny ; },
abstract = {VDAC2 (Voltage dependent anion channel 2) is a highly conserved pore-forming protein expressed in the outer membrane of eukaryotic mitochondria. In the present study, CgVDAC2 identified from Crassostrea gigas regulated the mitophagy of haemocytes induced by Vibrio splendidus. CgVDAC2 was distributed in the cytoplasm of three subpopulations of haemocytes. After V. splendidus stimulation, the mRNA and protein expressions of CgVDAC2 were induced in haemocytes. Furthermore, the green signals of CgVDAC2 were colocalized with the red signals of mitochondria and Mtphagy Dye, respectively. And their co-localization values were both increased significantly in haemocytes at 12 h after V. splendidus stimulation, respectively. In siCgVDAC2-treated oysters, the mRNA expressions of mitophagy-related genes (CgLC3, CgPINK1, CgParkin1, CgPHB2, and CgATG16L) and the levels of mitophagy decreased significantly in haemocytes after V. splendidus stimulation. In addition, both the fluorescence intensities of the JC-1 monomer/aggregate ratio (Q4/Q2) and mitochondrial reactive oxygen species (mtROS) increased significantly. Collectively, all the results indicated that CgVDAC2 participated in oyster antibacterial immune response through regulating the haemocyte mitophagy.},
}

Animals
*Vibrio/physiology
*Crassostrea/immunology/genetics
*Hemocytes/immunology
*Mitophagy/immunology
*Voltage-Dependent Anion Channel 2/genetics/immunology
Immunity, Innate/genetics
Gene Expression Regulation/immunology
Phylogeny

@article {pmid40027421,
year = {2025},
author = {Bagdonaitė, L and Mauvisseau, Q and Johnsen, A and Lifjeld, JT and Leder, EH},
title = {Sperm mtDNA Copy Number Is Not Associated With Midpiece Size Among Songbirds.},
journal = {Ecology and evolution},
volume = {15},
number = {3},
pages = {e71055},
pmid = {40027421},
issn = {2045-7758},
abstract = {Tremendous variation in sperm morphology is observed across the animal kingdom. Within avian taxa, the songbirds (infraorder Passerides) have the largest variation in sperm morphology. Their spermatozoa move by using energy generated in the midpiece, which is formed by multiple mitochondria fusing together during spermatogenesis. However, very little is known regarding the number of mitochondria required to form the songbird midpiece. Based on previous research showing an association of midpiece length and mitochondrial DNA (mtDNA) copy number in the zebra finch Taeniopygia guttata, we hypothesize that songbird species with longer sperm midpieces have more copies of mtDNA. We estimated the sperm mtDNA copy number in 19 species from 10 families within Passerides, covering a broad range of midpiece sizes. Mitochondrial and nuclear DNA abundance were determined using droplet digital PCR (ddPCR) and the ratio between mitochondrial and single-copy nuclear genes was used to estimate mtDNA copy number per spermatozoon. We found that species differ in their average mtDNA copy number, but the variation was small and not significantly related to midpiece length. A possible explanation is that mitochondrial genomes are eliminated in the spermatids during spermatogenesis.},
}

@article {pmid40027321,
year = {2025},
author = {Zhang, T and Fu, J and Li, C and Gong, R and Al-Rasheid, KAS and Stover, NA and Shao, C and Cheng, T},
title = {Novel findings on the mitochondria in ciliates, with description of mitochondrial genomes of six representatives.},
journal = {Marine life science & technology},
volume = {7},
number = {1},
pages = {79-95},
pmid = {40027321},
issn = {2662-1746},
abstract = {UNLABELLED: Determining and comparing mitochondrial genomes (mitogenomes) are essential for assessing the diversity and evolution of mitochondria. Ciliates are ancient and diverse unicellular eukaryotes, and thus are ideal models for elucidating the early evolution of mitochondria. Here, we report on six new mitogenomes of spirotrichs, a dominant ciliate group, and perform comparative analyses on 12 representative species. We show that: (1) the mitogenomes of spirotrichs are linear structures with high A+T contents (61.12-81.16%), bidirectional transcription, and extensive synteny (except for the nad5, ccmf and cob genes in Euplotia); (2) the non-split of NADH dehydrogenase subunit 2 gene (nad2) is a plesiomorphy of ciliates, whereas it has evolved into a split gene in Spirotrichea (apart from Euplotes taxa), Oligohymenophorea, and Armophorea; (3) the number of small subunit ribosomal proteins (rps) encoded in mitogenomes increases in the later branching classes of ciliates, whereas rps8 shows a loss trend during the evolution of Euplotes taxa; (4) the mitogenomes of spirotrichs exhibit A/T codon bias at the third position, and the codon bias is mainly due to DNA mutation in oligotrichs, hypotrichs and Diophrys appendiculata; (5) the phylogenetic position of D. appendiculata is unstable and controversial based on both phylogenetic analyses and mitogenome evidence. In summary, we investigated the mitogenome diversity of spirotrichs and broadened our understanding of the evolution of mitochondria in ciliates.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42995-024-00249-7.},
}

@article {pmid40022150,
year = {2025},
author = {Shalata, A and Saada, A and Mahroum, M and Hadid, Y and Furman, C and Shalata, ZE and Desnick, RJ and Lorber, A and Khoury, A and Higazi, A and Shaag, A and Barash, V and Spiegel, R and Vlodavsky, E and Rustin, P and Pietrokovski, S and Manov, I and Gieger, D and Tal, G and Salzberg, A and Mandel, H},
title = {Sengers syndrome caused by biallelic TIMM29 variants and RNAi silencing in Drosophila orthologue recapitulates the human phenotype.},
journal = {Human genomics},
volume = {19},
number = {1},
pages = {21},
pmid = {40022150},
issn = {1479-7364},
mesh = {Humans ; Animals ; Male ; Female ; *Drosophila melanogaster/genetics ; *Phenotype ; *Acidosis, Lactic/genetics/pathology ; *Drosophila Proteins/genetics ; Alleles ; Cataract/genetics/pathology ; RNA Interference ; Mutation/genetics ; Pedigree ; Cardiomyopathy, Hypertrophic/genetics/pathology ; Child ; Mitochondrial Precursor Protein Import Complex Proteins ; Muscular Diseases/genetics/pathology ; Mitochondria/genetics/pathology/metabolism ; Homozygote ; },
abstract = {PURPOSE: Sengers-syndrome (S.S) is a genetic disorder characterized by congenital cataracts, hypertrophic cardiomyopathy, skeletal myopathy and lactic acidosis. All reported cases were genetically caused by biallelic mutations in the AGK gene. We herein report a pathogenic variant in TIMM29 gene, encoding Tim29 protein, as a novel cause of S.S. Notably, AGK and Tim29 proteins are components of the TIM22 complex, which is responsible for importing carrier proteins into the inner mitochondrial membrane.

METHOD: Clinical data of 17 consanguineous patients featuring S.S was obtained. Linkage analysis, and sequencing were used to map and identify the disease-causing gene. Tissues derived from the study participants and a Drosophila melanogaster model were used to evaluate the effects of TIMM29 variant on S.S.

RESULTS: The patients presented with a severe phenotype of S.S, markedly elevated serum creatine-phosphokinase, combined mitochondrial-respiratory-chain-complexes deficiency, reduced pyruvate-dehydrogenase complex activity, and reduced adenine nucleotide translocator 1 protein. Histopathological studies showed accumulation of abnormal mitochondria. Homozygosity mapping and gene sequencing revealed a biallelic variant in TIMM29 NM_138358.4:c.514T > C NP_612367.1:p.(Trp172Arg). The knockdown of the Drosophila TIMM29 orthologous gene (CG14270) recapitulated the phenotype and pathology observed in the studied cohort. We expand the clinical phenotype of S.S and provide substantial evidence supporting TIMM29 as the second causal gene of a severe type of S.S, designated as S.S- TIMM29.

CONCLUSION: The present study uncovers several biochemical differences between the two S.S types, including the hyperCPKemia being almost unique for S.S-TIMM29 cohort, the different frequency of MMRCC and PDHc deficiencies among the two S.S types. We propose to designate the S.S associated with TIMM29 homozygous variant as S.S-TIMM29.},
}

Humans
Animals
Male
Female
*Drosophila melanogaster/genetics
*Phenotype
*Acidosis, Lactic/genetics/pathology
*Drosophila Proteins/genetics
Alleles
Cataract/genetics/pathology
RNA Interference
Mutation/genetics
Pedigree
Cardiomyopathy, Hypertrophic/genetics/pathology
Child
Mitochondrial Precursor Protein Import Complex Proteins
Muscular Diseases/genetics/pathology
Mitochondria/genetics/pathology/metabolism
Homozygote

@article {pmid40021962,
year = {2025},
author = {Dong, S and Li, X and Liu, Q and Zhu, T and Tian, A and Chen, N and Tu, X and Ban, L},
title = {Comparative genomics uncovers evolutionary drivers of locust migratory adaptation.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {203},
pmid = {40021962},
issn = {1471-2164},
support = {2022YFD1400500//National Key Research and Development Program of China/ ; },
mesh = {Animals ; *Animal Migration ; *Grasshoppers/genetics/physiology ; *Genomics/methods ; Adaptation, Physiological/genetics ; Evolution, Molecular ; Selection, Genetic ; Phylogeny ; Phenotype ; Biological Evolution ; Energy Metabolism/genetics ; },
abstract = {BACKGROUND: Locust migration is one of the main causes of locust plagues. While existing research has highlighted the adaptive migratory capabilities of locusts, the evolutionary patterns of their migration remain elusive. This study aims to explore these evolutionary patterns of locust migratory behavior at the genomic level. To achieve this, we conducted comparative genomics analysis using genomic data from 10 locust species with diverse migratory tendencies.

RESULTS: We identified 1064 genes showing signatures of positive selection in five migratory locust species using a dN/dS model. The BUSTED-PH model revealed 116 genes associated with migratory phenotypes. Gene ontology enrichment analysis indicated that these genes were predominantly related to metabolism and mitochondria-related pathways through both methods. Additionally, the evolutionary rate (RER) analysis between migratory and non-migratory locusts revealed significant divergence in energy metabolism pathways. Notably, of the genes analyzed, the SETX gene consistently showed evidence of positive selection across all five migratory species.

CONCLUSIONS: The findings suggest that the evolution of migratory behavior is associated with increased selective pressure on metabolism and mitochondria-related pathways. Hundreds of genes undergo selective changes during repetitive transitions to migratory behavior. These findings enhance our understanding of the genetic and phenotypic relationships underlying different locust migratory behaviors, providing important data for understanding the biological mechanisms behind locust outbreaks.},
}

Animals
*Animal Migration
*Grasshoppers/genetics/physiology
*Genomics/methods
Adaptation, Physiological/genetics
Evolution, Molecular
Selection, Genetic
Phylogeny
Phenotype
Biological Evolution
Energy Metabolism/genetics

@article {pmid40008059,
year = {2025},
author = {Nielsen, TL and Nielsen, SH and Novosolov, M and Gravlund, P and Allentoft, ME},
title = {Deeply Diverged but Morphologically Conserved Lineages in Tornier's Cat Snake (Crotaphopeltis tornieri) of the Eastern Arc Mountains.},
journal = {Ecology and evolution},
volume = {15},
number = {2},
pages = {e70452},
pmid = {40008059},
issn = {2045-7758},
abstract = {The Eastern Arc Mountain (EAM) forests in Tanzania have remarkably high endemism. Closely-related forest-adapted species are found isolated on different "sky islands" testifying to allopatry as a major driver for speciation in this region. However, some species defy this pattern. Tornier's cat snake (Crotaphopeltis tornieri) occupies most of the isolated mountain rainforest, despite presumably not being able to move across the arid savannah landscape that separates them. To test contrasting hypotheses of recent dispersal vs morphological conservatism we examined scale characters of 218 C. tornieri individuals and sequenced 80 full mitochondrial genomes covering populations from eight mountain blocks across the EAM and Southern Highlands of Tanzania (SHT). The morphological examination revealed no differentiation between populations except the Usambara Mountain populations showing significant differences in some scale characters. This was in stark contrast to the genetic analyses showing very high divergence between mountain populations. On average the mitochondrial genome showed > 12% genetic differentiation with cytB and COI showing interpopulation distances of up to 28.5% and 15.1%, respectively. Both Bayesian coalescent and maximum-likelihood based phylogenies, uncovered a highly distinct clade structure in C. tornieri defined by the mountains. Divergence times were estimated at c. 21 million years for the split between the EAM and SHT populations and 5.4-1.4 millions years for population splits within EAM. Our results point towards old isolation events but with a highly conserved morphology resulting in just one recognized species. By including presumed outgroups of C. degeni and C. hotamboeia in the phylogeny we found C. tornieri to be paraphyletic. These results have implications for understanding evolution in the EAM and warrant a revision of the number of species in this genus.},
}

@article {pmid40006901,
year = {2025},
author = {Stefano, GB and Kream, RM},
title = {Primordial Biochemicals Within Coacervate-Like Droplets and the Origins of Life.},
journal = {Viruses},
volume = {17},
number = {2},
pages = {},
pmid = {40006901},
issn = {1999-4915},
mesh = {*Mitochondria/metabolism ; *Viruses/metabolism/genetics ; *Origin of Life ; Humans ; Energy Metabolism ; },
abstract = {An organism is considered "alive" if it can grow, reproduce, respond to external stimuli, metabolize nutrients, and maintain stability. By this definition, both mitochondria and viruses exhibit the key characteristics of independent life. In addition to their capacity for self-replication under specifically defined conditions, both mitochondria and viruses can communicate via shared biochemical elements, alter cellular energy metabolism, and adapt to their local environment. To explain this phenomenon, we hypothesize that early viral prototype species evolved from ubiquitous environmental DNA and gained the capacity for self-replication within coacervate-like liquid droplets. The high mutation rates experienced in this environment streamlined their acquisition of standard genetic codes and adaptation to a diverse set of host environments. Similarly, mitochondria, eukaryotic intracellular organelles that generate energy and resolve oxygen toxicity, originally evolved from an infectious bacterial species and maintain their capacity for active functionality within the extracellular space. Thus, while mitochondria contribute profoundly to eukaryotic cellular homeostasis, their capacity for freestanding existence may lead to functional disruptions over time, notably, the overproduction of reactive oxygen species, a phenomenon strongly linked to aging-related disorders. Overall, a more in-depth understanding of the full extent of the evolution of both viruses and mitochondria from primordial precursors may lead to novel insights and therapeutic strategies to address neurodegenerative processes and promote healthy aging.},
}

*Mitochondria/metabolism
*Viruses/metabolism/genetics
*Origin of Life
Humans
Energy Metabolism

@article {pmid40002411,
year = {2025},
author = {Peña, FJ and Martín-Cano, FE and Becerro-Rey, L and da Silva-Álvarez, E and Gaitskell-Phillips, G and Aparicio, IM and Gil, MC and Ortega-Ferrusola, C},
title = {Redox Regulation and Glucose Metabolism in the Stallion Spermatozoa.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {14},
number = {2},
pages = {},
doi = {10.3390/antiox14020225},
pmid = {40002411},
issn = {2076-3921},
abstract = {Stallion spermatozoa are cells which exhibit intense metabolic activity, where oxidative phosphorylation in the mitochondria is the primary ATP generator. However, metabolism must be viewed as a highly interconnected network of oxidation-reduction reactions that generate the energy necessary for life. An unavoidable side effect of metabolism is the generation of reactive oxygen species, leading to the evolution of sophisticated mechanisms to maintain redox homeostasis. In this paper, we provide an updated overview of glucose metabolism in stallion spermatozoa, highlighting recent evidence on the role of aerobic glycolysis in these cells, and the existence of an intracellular lactate shuttle that may help to explain the particular metabolism of the stallion spermatozoa in the context of their redox regulation.},
}

@article {pmid40000832,
year = {2025},
author = {Du, W and Sun, Q and Hu, S and Yu, P and Kan, S and Zhang, W},
title = {Equus mitochondrial pangenome reveals independent domestication imprints in donkeys and horses.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {6803},
pmid = {40000832},
issn = {2045-2322},
support = {ZR2023QC278//Natural Science Foundation of Shandong Province/ ; 2022YFC3341002-2//National Key Research and Development Program of China/ ; },
mesh = {Animals ; *Equidae/genetics ; *Genome, Mitochondrial ; *Domestication ; Horses/genetics ; *Phylogeny ; Genetic Variation ; Mitochondria/genetics ; Animals, Domestic/genetics ; },
abstract = {Mitochondria are semi-autonomous organelles that play a crucial role in the energy budget of animal cells and are closely related to the locomotor abilities of animals. Equidae is renowned for including two domesticated species with distinct purposes: the endurance-oriented donkey and the power-driven horse, making it an ideal system for studying the relationship between mitochondria and locomotor abilities. In this study, to cover the genetic diversity of donkeys, we sequenced and assembled six new mitochondrial genomes from China. Meanwhile, we downloaded the published mitochondrial genomes of all species within Equus and conducted a comprehensive pan-mitochondrial genome analysis. We found that the mitochondrial genomes of Equus are highly conserved, each encoding 37 genes, including 13 protein-coding genes (PCGs). Phylogenetic analysis based on mitochondrial genomes supports previous research, indicating that the extant species in Equus are divided into three main branches: horses, donkeys, and zebras. Specifically, 761 genetic variants were identified between donkeys and horses, 68 of which were non-synonymous mutations in PCGs, potentially linked to their different locomotor abilities. Structural protein modeling indicated that despite genetic differences, the overall protein structures between donkeys and horses remain similar. This study revealed the mitochondrial genome variation patterns of domesticated animals, offering novelty perspectives on domestication imprints. Additionally, it provides reliable candidate molecular markers for the identification of donkeys and horses.},
}

Animals
*Equidae/genetics
*Genome, Mitochondrial
*Domestication
Horses/genetics
*Phylogeny
Genetic Variation
Mitochondria/genetics
Animals, Domestic/genetics

@article {pmid39998089,
year = {2025},
author = {Lan, X and Yang, M and Wang, J and Huang, C and Wu, A and Cui, L and Guo, Y and Zeng, L and Guo, X and Zhang, Y and Xiang, Y and Wang, Q},
title = {Pore-Forming Protein LIN-24 Enhances Starvation Resilience in Caenorhabditis elegans by Modulating Lipid Metabolism and Mitochondrial Dynamics.},
journal = {Toxins},
volume = {17},
number = {2},
pages = {},
pmid = {39998089},
issn = {2072-6651},
support = {82471591, 82460283, 32360136//National Natural Science Foundation of China/ ; 2023YFC3603300, 2023YFF1001000//National Key R&D Program, Ministry of Science and Technology of China/ ; 2024SSY07161 and 20221ZDG020070//Natural Science Foundation of Jiangxi Province/ ; 28740105//Foundation of Nanchang University/ ; },
mesh = {Animals ; *Caenorhabditis elegans/genetics/physiology/metabolism ; *Caenorhabditis elegans Proteins/genetics/metabolism ; *Lipid Metabolism ; *Mitochondrial Dynamics ; *Starvation/metabolism ; Mitochondria/metabolism ; },
abstract = {The ability to survive starvation is a critical evolutionary adaptation, yet the molecular mechanisms underlying this capability remain incompletely understood. Pore-forming proteins (PFPs) are typically associated with immune defense, where they disturb the membranes of target cells. However, the role of PFPs in non-immune functions, particularly in metabolic and structural adaptations to starvation, is less explored. Here, we investigate the aerolysin-like PFP LIN-24 in Caenorhabditis elegans and uncover its novel function in enhancing starvation resistance. We found that LIN-24 expression is upregulated during starvation, leading to increased expression of the lipase-encoding gene lipl-3. This upregulation accelerates the mobilization and degradation of lipid stores, thereby sustaining energy levels. Additionally, LIN-24 overexpression significantly preserves muscle integrity, as evidenced by the maintenance of muscle structure compared to wild-type worms. Furthermore, we demonstrate that LIN-24 induces the formation of donut-shaped mitochondria, a structural change likely aimed at reducing ATP production to conserve energy during prolonged nutrient deprivation. This mitochondrial remodeling depends on genes involved in mitochondrial dynamics, including mff-1, mff-2, drp-1, and clk-1. Collectively, these findings expand our understanding of PFPs, demonstrating their multifaceted role in stress resistance beyond immune defense. LIN-24's involvement in regulating metabolism, preserving muscle structure, and remodeling mitochondria highlights its crucial role in the adaptive response to starvation, offering novel insights into the evolution of stress resistance mechanisms and potential therapeutic targets for conditions related to muscle preservation and metabolic regulation.},
}

Animals
*Caenorhabditis elegans/genetics/physiology/metabolism
*Caenorhabditis elegans Proteins/genetics/metabolism
*Lipid Metabolism
*Mitochondrial Dynamics
*Starvation/metabolism
Mitochondria/metabolism

@article {pmid39990427,
year = {2025},
author = {Cai, L and Havird, JC and Jansen, RK},
title = {Recombination and retroprocessing in broomrapes reveal a universal roadmap for mitochondrial evolution in heterotrophic plants.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.02.14.637881},
pmid = {39990427},
issn = {2692-8205},
abstract = {The altered life history strategies of heterotrophic organisms often leave a profound genetic footprint on energy metabolism related functions. In parasitic plants, the reliance on host-derived nutrients and loss of photosynthesis in holoparasites have led to highly degraded to absent plastid genomes, but its impact on mitochondrial genome (mitogenome) evolution has remained controversial. By examining mitogenomes from 45 Orobanchaceae species including three independent transitions to holoparasitism and key evolutionary intermediates, we identified measurable and predictable genetic alterations in genomic shuffling, RNA editing, and intracellular (IGT) and horizontal gene transfer (HGT) en route to a nonphotosynthetic lifestyle. In-depth comparative analyses revealed DNA recombination and repair processes, especially RNA-mediated retroprocessing, as significant drivers for genome structure evolution. In particular, we identified a novel RNA-mediated IGT and HGT mechanism, which has not been demonstrated in cross-species and inter-organelle transfers. Based on this, we propose a generalized dosage effect mechanism to explain the biased transferability of plastid DNA to mitochondria across green plants, especially in heterotrophic lineages like parasites and mycoheterotrophs. Evolutionary rates scaled with these genomic changes, but the direction and strength of selection varied substantially among genes and clades, resulting in high contingency in mitochondrial genome evolution. Finally, we describe a universal roadmap for mitochondrial evolution in heterotrophic plants where increased recombination and repair activities, rather than relaxed selection alone, lead to differentiated genome structure compared to free-living species.},
}

@article {pmid39988053,
year = {2025},
author = {Monesi, N and Fernandes, GM and Valer, FB and Cardoso Uliana, JV and Trinca, V and Caleiro Seixas Azzolini, AE and Gorab, E and Alberici, LC},
title = {Identification and characterization of a laterally transferred alternative oxidase (AOX) in a terrestrial insect, the dipteran Pseudolycoriella hygida.},
journal = {Biochimie},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.biochi.2025.02.007},
pmid = {39988053},
issn = {1638-6183},
abstract = {Alternative oxidase (AOX) (EC 1.10.3.11) is a terminal oxidase in the mitochondrial inner membrane that branches the canonical electron transport system (ETS). AOX is ubiquitous in plants, frequently found in fungi and protists and presents a more sporadic distribution in metazoans. More recently, AOX has gained attention due to its potential application in gene therapy for treatment of mitochondrial diseases. Here we characterized the AOX in the basal Dipteran, Pseudolycoriella hygida using a combination of genomic analyses, molecular, functional and in vivo survival assays. AOX is a single copy gene that encodes three developmental stage specific protein isoforms. AOX localizes to the mitochondria in adult thoracic muscles, which present cyanide-resistant respiration that is sensitive to the AOX inhibitor salicylhydroxamic acid (SHAM). Both the cyanide-resistant respiration and AOX levels gradually increase during aging, but are not influenced by thermal stress. Thoracic mitochondria respire using substrates derived from several metabolic routes, such as pyruvate, proline, acylcarnitine, NADH and glycerol-3P, and present values of oxidative phosphorylation capacity ((P-L)/E = 0.70) and coupling (P/L = 4.35; L/E = 0.21). Adult flies exhibit a high survival resistance for SHAM-sensitive complex III inhibition. Together, our results demonstrate the presence of a functional AOX in a terrestrial arthropod and provide insights regarding AOX function in animals and evolution of respiratory systems in metazoans. Psl. hygida emerges as a natural and valuable model for comprehensive AOX research at the whole-organism level which complements models expressing the heterologous enzyme.},
}

@article {pmid39980242,
year = {2025},
author = {Yonemitsu, MA and Sevigny, JK and Vandepas, LE and Dimond, JL and Giersch, RM and Gurney-Smith, HJ and Abbott, CL and Supernault, J and Withler, R and Smith, PD and Weinandt, SA and Garrett, FES and Child, ZJ and Sigo, RLW and Unsell, E and Crim, RN and Metzger, MJ},
title = {Multiple Lineages of Transmissible Neoplasia in the Basket Cockle (C. nuttallii) With Repeated Horizontal Transfer of Mitochondrial DNA.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e17682},
doi = {10.1111/mec.17682},
pmid = {39980242},
issn = {1365-294X},
support = {//National Research Council/ ; 2208081//Division of Ocean Sciences/ ; A19AP00215//Bureau of Indian Affairs/ ; },
abstract = {Transmissible cancers are clonal lineages of neoplastic cells able to infect multiple hosts, spreading through populations in the environment as an infectious disease. Transmissible cancers have been identified in Tasmanian devils, dogs, and bivalves. Several lineages of bivalve transmissible neoplasias (BTN) have been identified in multiple bivalve species. In 2019 in Puget Sound, Washington, USA, disseminated neoplasia was observed in basket cockles (Clinocardium nuttallii), a species that is important to the culture and diet of the Suquamish Tribe as well as other tribes with traditional access to the species. To test whether disseminated neoplasia in cockles is a previously unknown lineage of BTN, a nuclear locus was amplified from cockles from Agate Pass, Washington, and sequences revealed evidence of transmissible cancer in several individuals. We used a combination of cytology and quantitative PCR to screen collections of cockles from 11 locations in Puget Sound and along the Washington coastline to identify the extent of contagious cancer spread in this species. Two BTN lineages were identified in these cockles, with one of those lineages (CnuBTN1) being the most prevalent and geographically widespread. Within the CnuBTN1 lineage, multiple nuclear loci support the conclusion that all cancer samples form a single clonal lineage. However, the mitochondrial alleles in each cockle with CnuBTN1 are different from each other, suggesting mitochondrial genomes of this cancer have been replaced multiple times during its evolution, through horizontal transmission. The identification and analysis of these BTNs are critical for broodstock selection, management practices, and repopulation of declining cockle populations, which will enable continued cultural connection and dietary use of the cockles by Coast Salish Tribes.},
}

@article {pmid39977315,
year = {2025},
author = {Elling, FJ and Pierrel, F and Chobert, SC and Abby, SS and Evans, TW and Reveillard, A and Pelosi, L and Schnoebelen, J and Hemingway, JD and Boumendjel, A and Becker, KW and Blom, P and Cordes, J and Nathan, V and Baymann, F and Lücker, S and Spieck, E and Leadbetter, JR and Hinrichs, KU and Summons, RE and Pearson, A},
title = {A novel quinone biosynthetic pathway illuminates the evolution of aerobic metabolism.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {8},
pages = {e2421994122},
doi = {10.1073/pnas.2421994122},
pmid = {39977315},
issn = {1091-6490},
support = {1702262//NSF (NSF)/ ; 1843285//NSF (NSF)/ ; NA//Gordon and Betty Moore Foundation (GBMF)/ ; 441217575//Deutsche Forschungsgemeinschaft (DFG)/ ; ANR-21-CE02-0018//Agence Nationale de la Recherche (ANR)/ ; ANR-15-IDEX-02//Agence Nationale de la Recherche (ANR)/ ; IDEX-IRS 2020//Grenoble-Alpes University/ ; EXC-2077-390741603//Deutsche Forschungsgemeinschaft (DFG)/ ; NA//Alexander von Humboldt-Stiftung (AvH)/ ; 016.Vidi.189.050//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO)/ ; 18-EXXO18-0039//NASA | NASA Astrobiology Institute (NAI)/ ; 946150//EC | European Research Council (ERC)/ ; 80NSSC19K0480//NASA | NASA Astrobiology Institute (NAI)/ ; },
mesh = {Aerobiosis ; *Biosynthetic Pathways ; Quinones/metabolism ; Plastoquinone/metabolism ; Oxidation-Reduction ; Biological Evolution ; Phylogeny ; Bacteria/metabolism/genetics ; Cyanobacteria/metabolism/genetics ; Evolution, Molecular ; },
abstract = {The dominant organisms in modern oxic ecosystems rely on respiratory quinones with high redox potential (HPQs) for electron transport in aerobic respiration and photosynthesis. The diversification of quinones, from low redox potential (LPQ) in anaerobes to HPQs in aerobes, is assumed to have followed Earth's surface oxygenation ~2.3 billion years ago. However, the evolutionary origins of HPQs remain unresolved. Here, we characterize the structure and biosynthetic pathway of an ancestral HPQ, methyl-plastoquinone (mPQ), that is unique to bacteria of the phylum Nitrospirota. mPQ is structurally related to the two previously known HPQs, plastoquinone from Cyanobacteriota/chloroplasts and ubiquinone from Pseudomonadota/mitochondria, respectively. We demonstrate a common origin of the three HPQ biosynthetic pathways that predates the emergence of Nitrospirota, Cyanobacteriota, and Pseudomonadota. An ancestral HPQ biosynthetic pathway evolved ≥ 3.4 billion years ago in an extinct lineage and was laterally transferred to these three phyla ~2.5 to 3.2 billion years ago. We show that Cyanobacteriota and Pseudomonadota were ancestrally aerobic and thus propose that aerobic metabolism using HPQs significantly predates Earth's surface oxygenation. Two of the three HPQ pathways were later obtained by eukaryotes through endosymbiosis forming chloroplasts and mitochondria, enabling their rise to dominance in modern oxic ecosystems.},
}

Aerobiosis
*Biosynthetic Pathways
Quinones/metabolism
Plastoquinone/metabolism
Oxidation-Reduction
Biological Evolution
Phylogeny
Bacteria/metabolism/genetics
Cyanobacteria/metabolism/genetics
Evolution, Molecular

@article {pmid39972273,
year = {2025},
author = {Zhou, B and Sui, R and Yu, L and Qi, D and Fu, S and Luo, Y and Qi, H and Li, X and Zhao, K and Liu, S and Tian, F},
title = {Transcriptomics and proteomics provide insights into the adaptative strategies of Tibetan naked carps (Gymnocypris przewalskii) to saline-alkaline variations.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {162},
pmid = {39972273},
issn = {1471-2164},
support = {32071489//National Natural Science Foundation of China/ ; 32401305//National Natural Science Foundation of China/ ; LHZX-2021-03//Joint Foundation from the Chinese Academy of Sciences -People's Government of Qinghai Province on Sanjiangyuan National Park/ ; LHZX-2021-03//Joint Foundation from the Chinese Academy of Sciences -People's Government of Qinghai Province on Sanjiangyuan National Park/ ; },
mesh = {Animals ; *Proteomics/methods ; *Salinity ; *Gills/metabolism ; Carps/genetics/metabolism ; Transcriptome ; Adaptation, Physiological/genetics ; Gene Expression Profiling ; Kidney/metabolism ; Alkalies ; Fish Proteins/genetics/metabolism ; Proteome/metabolism ; Tibet ; Osmoregulation/genetics ; Lakes ; },
abstract = {Gymnocypris przewalskii is an exclusively cyprinid fish that inhabits Lake Qinghai, which is characterized by high salinity and alkalinity. To elucidate the molecular basis of the adaptation of G. przewalskii to a wide range of salinity‒alkalinity conditions, we performed morphological, biochemical, transcriptomic and proteomic analyses of the major osmoregulatory organs of the gills and kidney. Morphological examination revealed that mitochondria-rich cells were replaced by mucus cells in the gills during the transition of G. przewalskii from freshwater to lake water. In the kidney, the tight junction formed dense structure in the renal tubules under lake water condition compared with the loose structure in freshwater. The results of the biochemical assays revealed an increased content of total amino acids, indicating their potential roles as osmolytes and energy supplies in freshwater. The decreased urea concentration suggested that urea synthesis might not be involved in the detoxicity of ammonia. The transcriptomic and proteomic data revealed that genes involved in ion absorption and ammonia excretion were activated in freshwater and that genes involved in cell junction and glutamine synthesis were induced in lake water, which was consistent with the morphological and biochemical observations. Together with the higher levels of glutamine and glutamate, we proposed that G. przewalskii alleviated the toxic effect of ammonia direct excretion through gills under freshwater and the activation of the conversion of glutamate to glutamine under high saline-alkaline condition. Our results revealed different expression profiles of genes involved in metabolic pathways, including the upregulation of genes involved in energy production in freshwater and the induction of genes involved in the synthesis of acetylneuramic acid and sphingolipid in soda lake water. In conclusion, the appearance of mitochondria-rich cells and increased energy production might contribute to ion absorption in G. przewalskii to maintain ion and solute homeostasis in freshwater. The existence of mucus cells and dense junctions, which are associated with increased gene expression, might be related to the adaptation of G. przewalskii to high salinity-alkalinity.},
}

Animals
*Proteomics/methods
*Salinity
*Gills/metabolism
Carps/genetics/metabolism
Transcriptome
Adaptation, Physiological/genetics
Gene Expression Profiling
Kidney/metabolism
Alkalies
Fish Proteins/genetics/metabolism
Proteome/metabolism
Tibet
Osmoregulation/genetics
Lakes

@article {pmid39962375,
year = {2025},
author = {Kim, SC and Kang, ES and Kim, TH and Choi, YR and Kim, HJ},
title = {Report on the complete organelle genomes of Orobanche Filicicola Nakai ex Hyun, Y. S. Lim & H. C. Shin (Orobanchaceae): insights from comparison with Orobanchaceae plant genomes.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {157},
pmid = {39962375},
issn = {1471-2164},
mesh = {*Genome, Mitochondrial ; *Phylogeny ; *Genome, Chloroplast ; Base Composition ; Orobanchaceae/genetics/classification ; Orobanche/genetics ; Genome, Plant ; Evolution, Molecular ; },
abstract = {BACKGROUND: Orobanche is a parasitic plant distributed in the temperate zone of Northern Hemisphere, with approximately 200 species found worldwide. In the Republic of Korea, two species of Orobanche, namely O. coerulescens Stephan ex Willd. and O. filicicola Nakai ex Hyun, Y. S. Lim & H. C. Shin, are present, with O. filicicola being endemic. Genome analysis of this species has not yet been performed, and characterizing its complete organelle genome will provide valuable insights into the phylogeny and genome evolution of parasitic plants.

RESULTS: The chloroplast and mitochondrial genomes were analyzed, revealing distinct characteristics. The chloroplast genome is 91,529 bp long with a GC content of 33.6%, containing 33 protein-coding, 30 tRNA, and 4 rRNA genes. In contrast, the mitochondrial genome is 1,058,991 bp long with a GC content of 45.5%, featuring 31 protein-coding, 16 tRNA, and 3 rRNA genes. The mitochondrial genome has over three times more simple sequence repeats and longer long repeats than the chloroplast genome. Analysis of synonymous codon usage in protein-coding genes from nine Orobanchaceae species revealed significant differences between chloroplasts and mitochondria, with codons ending in A or T exhibiting higher coding rates. Ka/Ks ratio calculations indicated that psbI and atpB had the smallest and largest ratios in chloroplasts, respectively, while ccmFC was identified as the only gene under positive selection in mitochondria genomes. Sequence alignment identified 30 homologous fragments between the two genomes, totaling 7,247 bp. Comparison of O. filicicola's chloroplast genome with related species showed gene loss and conserved inverted repeat sequences. Numerous homologous collinear blocks were found in mitochondrial genomes of related species, but some regions lacked homology. Phylogenetic analysis indicated identical topologies for chloroplasts and mitochondria, with Orobanchaceae forming a strong monophyletic group.

CONCLUSIONS: Characterizing the complete organelle genome of O. filicicola enabled a comprehensive analysis of the Orobanchaceae organelle genome, providing important baseline data for its structure and evolution.},
}

*Genome, Mitochondrial
*Phylogeny
*Genome, Chloroplast
Base Composition
Orobanchaceae/genetics/classification
Orobanche/genetics
Genome, Plant
Evolution, Molecular

@article {pmid39961891,
year = {2025},
author = {Larkum, AWD and Falkowski, PG and Edwards, D and Osmond, CB and Lambers, H and Sanchez-Baracaldo, P and Ritchie, RJ and Runcie, JW and Ralph, PJ and Westoby, M and Maberly, S and Griffiths, H and Smith, FA and Beardall, J},
title = {John Raven, FRS, FRSE: a truly great innovator in plant physiology, photosynthesis and much more.},
journal = {Photosynthesis research},
volume = {163},
number = {2},
pages = {18},
pmid = {39961891},
issn = {1573-5079},
mesh = {*Photosynthesis/physiology ; History, 20th Century ; History, 21st Century ; Plant Physiological Phenomena ; Botany/history ; },
abstract = {This is a tribute to a truly inspirational plant biologist, Prof. John A. Raven, FRS, FRSE (25th June 1941- 23rd May 2024), who died at the age of 82. He was a leader in the field of evolution and physiology of algae and land plants. His research touched on many areas including photosynthesis, ion transport, carbon utilisation, mineral use, such as silicon, iron and molybdenum, the evolution of phytoplankton, the evolution of root systems, the impact of global change, especially on the acidification of the oceans, carbon gain and water use in early land plants, and ways of detecting extraterrestrial photosynthesis. Beginning his research career in the Botany School, University of Cambridge, John studied ion uptake in a giant algal cell. This was at the time of great strides brought about by Peter Mitchell (1920-1992) in elucidating the role of energy generation in mitochondria and chloroplasts and the coupling of ion transport systems to energy generation. With Enid MacRobbie and Andrew Smith, John pioneered early work on the involvement of ion transport in the growth and metabolism of plant cells.On leaving Cambridge John took up a lectureship at the University of Dundee in 1971, where he was still attached upon his death. His primary focus over the years, with one of us (Paul Falkowski), was on phytoplankton, the photosynthetic microalgae of the oceans. Still, his publication list of 5 books and over 600 scientific papers spans a very broad range. The many highly cited papers (see Table 1) attest to an outstanding innovator, who influenced a multitude of students and coworkers and a very wide readership worldwide. At the personal level, John Raven was a wonderful human being; he had an extraordinary memory, dredging up facts and little-known scientific papers, like a scientific magician, but at the same time making humorous jokes and involving his colleagues in fun and sympathetic appreciation. Table 1 Ten best cited articles (from google scholar) Citations Date Aquatic Photosynthesis, 3rd Edition P.G. Falkowski & J.A. Raven Princeton University Press, 2013 3854 2013 The evolution of modern eukaryotic phytoplankton P.G. Falkowski, M.E. Katz, A.H. Knoll, A. Quigg, J.A. Raven, et al Science 305, 354-360 1790 2004 CO2 concentrating mechanisms in algae: mechanisms, environmental modulation, and evolution M. Giordano, J. Beardall & J.A. Raven Annu. Rev. Plant Biol. 56 (1), 99-131 1648 2005 Algae as nutritional food sources: revisiting our understanding M.L. Wells, P. Potin, J.S. Craigie, J.A. Raven, S.S. Merchant, et al Journal of applied phycology 29, 949-982 1527 2017 Plant Nutrient acquisition strategies change with soil age H. Lambers, J.A. Raven, G.R. Shaver & S.E. Smith Trends in ecology & evolution 23, 95-103 1488 2008 Ocean acidification due to increasing atmospheric carbon dioxide J. Raven, K. Caldeira, H. Elderfield, O. Hoegh-Guldberg, P. Liss, et al The Royal Society, Policy Document, June 2005 1470 2005 Phytoplankton in a changing world: cell size and elemental stoichiometry Z.V. Finkel, J. Beardall, K.J. Flynn, A. Quigg, T.A.V. Rees & J.A. Raven Journal of plankton research 32, 119-137 1198 2010 Opportunities for improving phosphorus efficiency in crop plants E.J. Veneklaas, H. Lambers, J. Bragg, P.M. Finnegan, C.E. Lovelock, et al New phytologist 195, 306-320 951 2012 Adaptation of unicellular algae to irradiance: an analysis of strategies K. Richardson, J. Beardall & J.A. Raven New Phytologist 93, 157-191 914 1983 Nitrogen assimilation and transport in vascular land plants in relation to Intracellular pH regulation J.A. Raven & F.A. Smith New Phytologist 76, 415-431 893 1976 Temperature and algal growth J.A. Raven & R.J. Geider New phytologist 110, 441-461 867 1988 The role of trace metals in photosynthetic electron transport in O2 -evolving organisms J.A. Raven, M.C.W. Evans & R.E. Korb Photosynthesis Research 60, 111-150 840 1999.},
}

*Photosynthesis/physiology
History, 20th Century
History, 21st Century
Plant Physiological Phenomena
Botany/history

@article {pmid39949038,
year = {2025},
author = {Ratajczak, MZ and Thetchinamoorthy, K and Wierzbicka, D and Konopko, A and Ratajczak, J and Kucia, M},
title = {Extracellular microvesicles/exosomes - magic bullets in horizontal transfer between cells of mitochondria and molecules regulating mitochondria activity.},
journal = {Stem cells (Dayton, Ohio)},
volume = {},
number = {},
pages = {},
doi = {10.1093/stmcls/sxae086},
pmid = {39949038},
issn = {1549-4918},
abstract = {Extracellular microvesicles (ExMVs) were one of the first communication platforms between cells that emerged early in evolution. Evidence indicates that all types of cells secrete these small circular structures surrounded by a lipid membrane that plays an important role in cellular physiology and some pathological processes. ExMVs interact with target cells and may stimulate them by ligands expressed on their surface and/or transfer to the target cells their cargo comprising various RNA species, proteins, bioactive lipids, and signaling nucleotides. These small vesicles can also hijack some organelles from the cells and, in particular, transfer mitochondria, which are currently the focus of scientific interest for their potential application in clinical settings. Different mechanisms exist for transferring mitochondria between cells, including their encapsulation in ExMVs or their uptake in a "naked" form. It has also been demonstrated that mitochondria transfer may involve direct cell-cell connections by signaling nanotubules. In addition, evidence accumulated that ExMVs could be enriched for regulatory molecules, including some miRNA species and proteins that regulate the function of mitochondria in the target cells. Recently, a new beneficial effect of mitochondrial transfer has been reported based on inducing the mitophagy process, removing damaged mitochondria in the recipient cells to improve their energetic state. Based on this novel role of ExMVs in powering the energetic state of target cells, we present a current point of view on this topic and review some selected most recent discoveries and recently published most relevant papers.},
}

@article {pmid39946260,
year = {2025},
author = {Waneka, G and Broz, AK and Wold-McGimsey, F and Zou, Y and Wu, Z and Sloan, DB},
title = {Disruption of recombination machinery alters the mutational landscape in plant organellar genomes.},
journal = {G3 (Bethesda, Md.)},
volume = {},
number = {},
pages = {},
doi = {10.1093/g3journal/jkaf029},
pmid = {39946260},
issn = {2160-1836},
support = {R35 GM148134/GM/NIGMS NIH HHS/United States ; },
abstract = {Land plant organellar genomes have extremely low rates of point mutation yet also experience high rates of recombination and genome instability. Characterizing the molecular machinery responsible for these patterns is critical for understanding the evolution of these genomes. While much progress has been made towards understanding recombination activity in land plant organellar genomes, the relationship between recombination pathways and point mutation rates remains uncertain. The organellar targeted mutS homolog MSH1 has previously been shown to suppress point mutations as well as non-allelic recombination between short repeats in Arabidopsis thaliana. We therefore implemented high-fidelity Duplex Sequencing to test if other genes that function in recombination and maintenance of genome stability also affect point mutation rates. We found small to moderate increases in the frequency of single nucleotide variants (SNVs) and indels in mitochondrial and/or plastid genomes of A. thaliana mutant lines lacking radA, recA1, or recA3. In contrast, osb2 and why2 mutants did not exhibit an increase in point mutations compared to wild type (WT) controls. In addition, we analyzed the distribution of SNVs in previously generated Duplex Sequencing data from A. thaliana organellar genomes and found unexpected strand asymmetries and large effects of flanking nucleotides on mutation rates in WT plants and msh1 mutants. Finally, using long-read Oxford Nanopore sequencing, we characterized structural variants in organellar genomes of the mutant lines and show that different short repeat sequences become recombinationally active in different mutant backgrounds. Together, these complementary sequencing approaches shed light on how recombination may impact the extraordinarily low point mutation rates in plant organellar genomes.},
}

@article {pmid39945506,
year = {2025},
author = {Van Gaever, M and Dupuy, O and Dupont, E and Canu, MH and Daussin, F},
title = {Early sensorimotor restriction in rats induces age-dependent mitochondrial alterations in skeletal muscles and brain structures.},
journal = {The Journal of physiology},
volume = {},
number = {},
pages = {},
doi = {10.1113/JP287765},
pmid = {39945506},
issn = {1469-7793},
abstract = {A sedentary lifestyle can lead to motor and cognitive deficits, increasing the risk of neurodegenerative diseases in ageing. Emerging hypotheses suggest that these functional alterations may be related to energy metabolism. Indeed, ATP produced by mitochondria is essential for muscle contraction, neurotransmission and brain plasticity processes. Although a sedentary lifestyle has been associated with mitochondrial alterations in skeletal muscle, the potential effects on brain structures have yet to be investigated. The present study aimed to determine whether early sensorimotor restriction (SMR) alters mitochondrial metabolism in rat muscles and brain structures. Enzyme activities of citrate synthase (CS) and respiratory chain complexes I, II and IV were measured using a spectrophotometric technique and mitochondrial respiration was assessed using high-resolution respirometry in two hind limb muscles [soleus and extensor digitorum longus (EDL)] and four brain structures (sensorimotor cortex, striatum, prefrontal cortex and hippocampus) in control rats and rats experiencing early SMR from birth to day 28. Mitochondrial enzyme activities decreased in the soleus (complexes I and II), in the EDL (complex I) and in the hippocampus (complexes I and IV) in an age-dependent manner, whereas no effect was observed in other brain structures. CS activity decreases in the soleus and increases transiently in the striatum and sensorimotor cortex at postnatal day 15. Mitochondrial respiration was reduced in the soleus and in the sensorimotor cortex (CI and CI+CII). Early SMR appears to induce quantitative and qualitative mitochondrial alterations in skeletal muscles and certain brain structures involved in cognitive and motor processes. KEY POINTS: Early sensorimotor restriction (SMR) alters mitochondrial enzyme activities and mitochondrial respiration in skeletal muscles and brain. Mitochondrial alterations induced by early SMR are age-dependent, structure-dependent and complex-dependent. Mitochondrial enzyme activities increase during development and the evolution pattern is specific to the different structures.},
}

@article {pmid39944907,
year = {2025},
author = {Ruiz, E and Leprieur, F and Sposito, G and Lüthi, M and Schmidlin, M and Panfili, J and Pellissier, L and Albouy, C},
title = {Environmental DNA Epigenetics Accurately Predicts the Age of Cultured Fish Larvae.},
journal = {Ecology and evolution},
volume = {15},
number = {2},
pages = {e70645},
pmid = {39944907},
issn = {2045-7758},
abstract = {While acquiring age information is crucial for efficient stock management and biodiversity conservation, traditional aging methods fail to offer a universal, non-invasive, and precise way of estimating a wild animal's age. DNA methylation from tissue DNA (tDNA) was recently proposed as a method to overcome these issues and showed more accurate results than telomere-length-based age assessments. Here, we used environmental DNA (eDNA) for the first time as a template for age estimation, focusing on the larval phase (10-24 days post-hatch) of cultured Dicentrarchus labrax (seabass), a species of major economic and conservation interest. Using third-generation sequencing, we were able to directly detect various modification types (e.g., cytosine and adenosine methylation in all contexts) across the whole genome using amplification-free nanopore sequencing. However, aging sites were only present in the mitogenome, which could be a specific feature of eDNA methylation or the consequence of better DNA protection within mitochondria. By considering qualitative and quantitative information about aging sites according to an objective model selection framework, our epigenetic clock reached a cross-validated accuracy of 2.6 days (Median Absolute Error). Such performances are higher than those of previous clocks, notably for adult seabass even when scaling MAE to the age range, which could be linked to a more dynamic epigenome during early life stages. Overall, our pilot study proposes new methods to determine the potential of eDNA for simultaneous age and biodiversity assessments, although robust validation of our preliminary results along with methodological developments are needed before field applications can be envisaged.},
}

@article {pmid39944804,
year = {2024},
author = {Vorozheykin, PS and Titov, II},
title = {Computer analysis shows differences between mitochondrial miRNAs and other miRNAs.},
journal = {Vavilovskii zhurnal genetiki i selektsii},
volume = {28},
number = {8},
pages = {834-842},
doi = {10.18699/vjgb-24-91},
pmid = {39944804},
issn = {2500-0462},
abstract = {A subclass of miRNAs with as yet unknown specific functions is mitomiRs - mitochondrial miRNAs that are mainly derived from nuclear DNA and are imported into mitochondria; moreover, changes in the expression levels of mitomiRs are associated with some diseases. To identify the most pronounced characteristics of mitochondrial miRNAs that distinguish them from other miRNAs, we classified mitomiR sequences using the Random Forest algorithm. The analysis revealed, for the first time, a significant difference between mitomiRs and other microRNAs by the following criteria (in descending order of importance in the classification): mitomiRs are evolutionarily older (have a lower phylostratigraphic age index, PAI); have more targets and disease associations, including mitochondrial ones (two-sided Fisher's exact test, average p-values 1.82 × 10-89/1.13 × 10-96 for all mRNA/diseases and 6.01 × 10-22/1.09 × 10-9 for mitochondria, respectively); and are in the class of "circulating" miRNAs (average p- value 1.20 × 10-56). The identified differences between mitomiRs and other miRNAs may help uncover the mode of miRNA delivery into mitochondria, indicate the evolutionary conservation and importance of mitomiRs in the regulation of mitochondrial function and metabolism, and generally show that mitomiRs are not randomly encountered miRNAs. Information on 1,312 experimentally validated mitomiR sequences for three organisms (Homo sapiens, Mus musculus and Rattus norvegicus) is collected in the mitomiRdb database (https://mitomiRdb.org).Key words: mitomiR; mitochondria; miRNA; evolution; database.},
}

@article {pmid39940743,
year = {2025},
author = {Zeng, Q and Yu, Q and Mo, Y and Liang, H and Chen, B and Meng, J},
title = {Genome-Wide Identification and Functional Characterization of the Acyl-CoA Dehydrogenase (ACAD) Family in Fusarium sacchari.},
journal = {International journal of molecular sciences},
volume = {26},
number = {3},
pages = {},
doi = {10.3390/ijms26030973},
pmid = {39940743},
issn = {1422-0067},
support = {31960031//National Natural Science Foundation of China/ ; 2024GXNSFAA010041//Guangxi Natural Science Foundation/ ; },
mesh = {*Fusarium/genetics/pathogenicity/enzymology ; *Phylogeny ; Fatty Acids/metabolism ; Fungal Proteins/genetics/metabolism ; Acyl-CoA Dehydrogenase/genetics/metabolism ; Genome, Fungal ; Gene Expression Regulation, Fungal ; Multigene Family ; Plant Diseases/microbiology/genetics ; },
abstract = {Fusarium sacchari is one of the primary causal agents of Pokkah boeng disease (PBD), an important disease of sugarcane worldwide. The acyl-CoA dehydrogenases (ACADs) constitute a family of flavoenzymes involved in the β-oxidation of fatty acids and amino acid catabolism in mitochondria. However, the role of ACADs in the pathogenesis of F. sacchari is unclear. Here, 14 ACAD-encoding genes (FsACAD-1-FsACAD-14) were identified by screening the entire genome sequence of F. sacchari. The FsACAD genes are distributed across seven chromosomes and were classified into seven clades based on phylogenetic analysis of the protein sequences. In vivo mRNA quantification revealed that the FsACAD genes are differentially expressed during sugarcane infection, and their expression patterns differ significantly in response to the in vitro induction of fatty acids of different classes. Fatty acid utilization assays of the FsACAD-deletion mutants revealed that the FsACADs varied in their preference and ability to break down different fatty acids and amino acids. There was variation in the adverse impact of FsACAD-deletion mutants on fungal traits, including growth, conidiation, stress tolerance, and virulence. These findings provide insights into the roles of FsACADs in F. sacchari, and the identification of FsACADs offers potential new targets for the improved control of PBD.},
}

*Fusarium/genetics/pathogenicity/enzymology
*Phylogeny
Fatty Acids/metabolism
Fungal Proteins/genetics/metabolism
Acyl-CoA Dehydrogenase/genetics/metabolism
Genome, Fungal
Gene Expression Regulation, Fungal
Multigene Family
Plant Diseases/microbiology/genetics

@article {pmid39936990,
year = {2025},
author = {Zhang, Y and Sun, J and Li, S and Wang, L and Song, L},
title = {The Potential Mechanism of Cuproptosis in Hemocytes of the Pacific Oyster Crassostrea gigas upon Elesclomol Treatment.},
journal = {Cells},
volume = {14},
number = {3},
pages = {},
pmid = {39936990},
issn = {2073-4409},
support = {32222086, 32230110//National Natural Science Foundation of China/ ; CARS-49//the fund for China Agriculture Research System/ ; No//Outstanding Talents and Innovative Teams of Agricultural Scientific Research in MARA/ ; LT202009//innovation team of Aquaculture Environment Safety from Liaoning Province/ ; XLYC2203087//Liaoning Revitalization Talents Program/ ; 2022RG14//Dalian High Level Talent Innovation Support Program/ ; 2022RY01//Dalian Outstanding Young Scientific and Technological Talent/ ; },
mesh = {Animals ; *Hemocytes/metabolism/drug effects ; *Crassostrea/drug effects/genetics ; *Copper/metabolism/pharmacology ; Mitochondria/metabolism/drug effects ; Cell Death/drug effects ; },
abstract = {Cuproptosis is a novel cell death dependent on mitochondrial respiration and regulated by copper. While the study of it is mainly focused on tumor therapy, in the present study, two key cuproptosis-related genes, ferredoxin (FDX1) and dihydrolipoamide S-acetyltransferase (DLAT) homologs (designated as CgFDX1 and CgDLAT), were identified from Crassostrea gigas. CgFDX1 has a Fer2 domain with a 2Fe-2S cluster forming a unique ferredoxin. CgDLAT is composed of a biotin_lipoyl domain, an E3-binding domain, and a 2-oxoacid_dh domain. CgFDX1 and CgDLAT mRNA were expressed in all the examined tissues. After elesclomol treatment, both mRNA and protein expressions of them were reduced in the hemocytes. The mortality rate of the hemocytes increased significantly, and the hemocytes were accompanied with noticeable adhesive abnormalities and heightened secretion after elesclomol treatment. Additionally, the accumulation or depletion of actin was observed in the hemocytes. The integrity of the double membrane structure of the mitochondria was compromised, and the organization of mitochondrial cristae was disrupted. The contents of copper, malondialdehyde (MDA), pyruvic acid and mitoSOX as well as the ratio of cells with low mitochondrial potential increased significantly in the hemocytes upon elesclomol treatment and the content of citric acid decreased significantly. These findings suggest the potential presence of cuproptosis in oysters and its activation mechanism is relatively conserved in evolution.},
}

Animals
*Hemocytes/metabolism/drug effects
*Crassostrea/drug effects/genetics
*Copper/metabolism/pharmacology
Mitochondria/metabolism/drug effects
Cell Death/drug effects

@article {pmid39933620,
year = {2025},
author = {Tatarczuch, A and Gogola-Mruk, J and Kotarska, K and Polański, Z and Ptak, A},
title = {Mitochondrial activity and steroid secretion in mouse ovarian granulosa cells are suppressed by a PFAS mixture.},
journal = {Toxicology},
volume = {512},
number = {},
pages = {154083},
doi = {10.1016/j.tox.2025.154083},
pmid = {39933620},
issn = {1879-3185},
abstract = {The accumulation of a number of per- and polyfluoroalkyl substances (PFASs) in ovarian follicular fluid (FF) has been documented, raising serious questions about their impact on female fertility. Here, we tested the hypothesis that a mixture of PFASs acts in a paracrine manner on granulosa cells (GCs) as a metabolism-disrupting chemical. We selected perfluorooctane sulfonate (PFOS; 22.4 ng/mL), perfluorooctanoic acid (PFOA; 14.5 ng/mL), perfluorohexane sulfonate (PFHxS; 21.3 ng/mL), perfluorodecanoic acid (PFDA; 0.9 ng/mL), perfluoroheptane sulphonate (PFHpA; 0.6 ng/mL), perfluoroundecanoic acid (PFUnDA; 0.4 ng/mL), and perfluorononanoic acid (PFNA; 2 ng/mL), which were the most commonly detected PFASs in FF of women undergoing assisted reproductive technology treatment. Exposure of mouse GCs to the PFAS mixture decreased the amount of active mitochondria and the mitochondrial membrane potential, which correlated with a reduction in ATP production and inhibition of oxidative phosphorylation (OXPHOS). At the same time, expression of the mitochondrial membrane-associated steroidogenic enzyme 3-beta-hydroxysteroid dehydrogenase (3βHSD) and production of the major steroids progesterone and estradiol were decreased. In addition, expression and activity of superoxide dismutase 1 (SOD1), an enzyme that neutralizes reactive oxygen species (ROS), were decreased while ROS levels and lipid peroxidation were increased without cell death, indicating that the PFAS mixture had subtoxic effects. Our results show that PFAS mixtures, at concentrations similar to those found in human FF led to GC dysfunction by impairing mitochondrial function and steroid secretions and therefore may have implications for reproductive health.},
}

@article {pmid39921600,
year = {2025},
author = {Shi, X and Ma, C and Chen, N and Xu, MM and Kambal, S and Cai, ZF and Yang, Q and Adeola, AC and Liu, LS and Wang, J and Lu, WF and Li, Y and Msalya, GM and Lei, C and Mwacharo, JM and Han, JL and Hanotte, O and Zhang, YP and Peng, MS},
title = {Selection increases mitonuclear DNA discordance but reconciles incompatibility in African cattle.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msaf039},
pmid = {39921600},
issn = {1537-1719},
abstract = {Mitochondrial function relies on the coordinated interactions between genes in the mitochondrial (mtDNA) and nuclear genomes. Imperfect interactions following mitonuclear incompatibility may lead to reduced fitness. MtDNA introgressions across species and populations are common and well documented. Various strategies may be expected to reconcile mitonuclear incompatibility in hybrids or admixed individuals. African admixed cattle (Bos taurus × B. indicus) show sex-biased admixture, with taurine (B. taurus) mtDNA and a nuclear genome predominantly of humped zebu (B. indicus). Here, we leveraged local ancestry inference approaches to identify the ancestry and distribution patterns of nuclear functional genes associated with the mitochondrial oxidative phosphorylation process in the genomes of African admixed cattle. We show that most of the nuclear genes involved in mitonuclear interactions are under selection and of humped zebu ancestry. Variation in mtDNA copy number (mtDNA-CN) may have contributed to the recovery of optimal mitochondrial function following admixture with the regulation of gene expression, alleviating or nullifying mitochondrial dysfunction. Interestingly, some nuclear mitochondrial genes with enrichment in taurine ancestry may have originated from ancient African aurochs (B. primigenius africanus) introgression. They may have contributed to the local adaptation of African cattle to pathogen burdens. Our study provides further support and new evidence showing that the successful settlement of cattle across the continent was a complex mechanism involving adaptive introgression, mtDNA-CN variation, regulation of gene expression, and selection of ancestral mitochondria-related genes.},
}

@article {pmid39906580,
year = {2025},
author = {Erkosar, B and Dupuis, C and Savary, L and Kawecki, TJ},
title = {Shared genetic architecture links energy metabolism, behavior and starvation resistance along a power-endurance axis.},
journal = {Evolution letters},
volume = {9},
number = {1},
pages = {150-162},
pmid = {39906580},
issn = {2056-3744},
abstract = {Shared developmental, physiological, and molecular mechanisms can generate strong genetic covariances across suites of traits, constraining genetic variability, and evolvability to certain axes in multivariate trait space ("variational modules" or "syndromes"). Such trait suites will not only respond jointly to selection; they will also covary across populations that diverged from one another by genetic drift. We report evidence for such a genetically correlated trait suite that links traits related to energy metabolism along a "power-endurance" axis in Drosophila melanogaster. The "power" pole of the axis is characterized by high potential for energy generation and expenditure-high expression of glycolysis and TCA cycle genes, high abundance of mitochondria, and high spontaneous locomotor activity. The opposite "endurance" pole is characterized by high triglyceride (fat) reserves, locomotor endurance, and starvation resistance (and low values of traits associated with the "power" pole). This trait suite also aligns with the first principal component of metabolome; the "power" direction is characterized by low levels of trehalose (blood sugar) and high levels of some amino acids and their derivatives, including creatine, a compound known to facilitate energy production in muscles. Our evidence comes from six replicate "Selected" populations adapted to a nutrient-poor larval diet regime during 250 generations of experimental evolution and six "Control" populations evolved in parallel on a standard diet regime. We found that, within each of these experimental evolutionary regimes, the above traits strongly covaried along this "power-endurance" axis across replicate populations which diversified by drift, indicating a shared genetic architecture. The two evolutionary regimes also drove divergence along this axis, with Selected populations on average displaced towards the "power" direction compared to Controls. Aspects of this "power-endurance" axis resemble the "pace of life" syndrome and the "thrifty phenotype"; it may have evolved as part of a coordinated organismal response to nutritional conditions.},
}

@article {pmid39903101,
year = {2025},
author = {Iliushchenko, D and Efimenko, B and Mikhailova, AG and Shamanskiy, V and Saparbaev, MK and Matkarimov, BT and Mazunin, I and Voronka, A and Knorre, D and Kunz, WS and Kapranov, P and Denisov, S and Fellay, J and Khrapko, K and Gunbin, K and Popadin, K},
title = {Deciphering the Foundations of Mitochondrial Mutational Spectra: Replication-Driven and Damage-Induced Signatures Across Chordate Classes.},
journal = {Molecular biology and evolution},
volume = {42},
number = {2},
pages = {},
pmid = {39903101},
issn = {1537-1719},
support = {//Federal Academic Leadership Program Priority 2030/ ; //Immanuel Kant Baltic Federal University/ ; 21-75-20143//Russian Science Foundation/ ; 075-15-2021-1084//Ministry of Science and Higher Education of the Russian Federation/ ; KU 911/22-1//Deutsche Forschungsgemeinschaft/ ; AP23485899//Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; },
mesh = {*DNA, Mitochondrial/genetics ; Animals ; *DNA Replication ; DNA Damage ; Mutation ; Mutagenesis ; DNA Repair ; Urochordata/genetics ; Cytochromes b/genetics ; DNA-Directed DNA Polymerase/genetics ; DNA Mismatch Repair ; },
abstract = {Mitochondrial DNA (mtDNA) mutagenesis remains poorly understood despite its crucial role in disease, aging, and evolutionary tracing. In this study, we reconstructed a comprehensive 192-component mtDNA mutational spectrum for chordates by analyzing 118,397 synonymous mutations in the CytB gene across 1,697 species and five classes. This analysis revealed three primary forces shaping mtDNA mutagenesis: (i) symmetrical, replication-driven errors by mitochondrial polymerase (POLG), resulting in C > T and A > G mutations that are highly conserved across classes; (ii) asymmetrical, damage-driven C > T mutations on the single-stranded heavy strand with clock-like dynamics; and (iii) asymmetrical A > G mutations on the heavy strand, with dynamics suggesting sensitivity to oxidative damage. The third component, sensitive to oxidative damage, positions mtDNA mutagenesis as a promising marker for metabolic and physiological processes across various classes, species, organisms, tissues, and cells. The deconvolution of the mutational spectra into mutational signatures uncovered deficiencies in both base excision repair (BER) and mismatch repair (MMR) pathways. Further analysis of mutation hotspots, abasic sites, and mutational asymmetries underscores the critical role of single-stranded DNA damage (components ii and iii), which, uncorrected due to BER and MMR deficiencies, contributes roughly as many mutations as POLG-induced errors (component i).},
}

*DNA, Mitochondrial/genetics
Animals
*DNA Replication
DNA Damage
Mutation
Mutagenesis
DNA Repair
Urochordata/genetics
Cytochromes b/genetics
DNA-Directed DNA Polymerase/genetics
DNA Mismatch Repair

@article {pmid39901091,
year = {2025},
author = {Park, S and Hwang, Y and Kim, H and Choi, K},
title = {Insights into the nuclear-organelle DNA integration in Cicuta virosa (Apiaceae) provided by complete plastid and mitochondrial genomes.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {102},
pmid = {39901091},
issn = {1471-2164},
mesh = {*Genome, Mitochondrial ; *Genome, Plastid ; *Cell Nucleus/genetics ; *Apiaceae/genetics ; Phylogeny ; Evolution, Molecular ; Genome, Plant ; DNA, Plant/genetics ; Plastids/genetics ; },
abstract = {BACKGROUND: Gene transfer between the organelles and the nucleus plays a central role in shaping plant genome evolution. The identification and analysis of nuclear DNA of plastid (NUPTs) and mitochondrial (NUMTs) origins are important for exploring the extent of intracellular DNA transfer in genomes.

RESULTS: We report the complete plastid and mitochondrial genomes (plastome and mitogenome) of Cicuta virosa (Apiaceae) as well as a draft nuclear genome using high-fidelity (HiFi) PacBio sequencing technologies. The C. virosa plastome (154,449 bp) is highly conserved, with a quadripartite structure, whereas the mitogenome (406,112 bp) exhibits two chromosomes (352,718 bp and 53,394 bp). The mitochondrial-encoded genes (rpl2, rps14, rps19, and sdh3) were successfully transferred to the nuclear genome. Our findings revealed extensive DNA transfer from organelles to the nucleus, with 6,686 NUPTs and 6,237 NUMTs detected, covering nearly the entire plastome (99.93%) and a substantial portion of the mitogenome (77.04%). These transfers exhibit a range of sequence identities (80-100%), suggesting multiple transfer events over evolutionary timescales. Recent DNA transfer between organelles and the nucleus is more frequent in mitochondria than that in plastids.

CONCLUSIONS: This study contributes to the understanding of ongoing genome evolution in C. virosa and underscores the significance of the organelle-nuclear genome interplay in plant species. Our findings provide valuable insights into the evolutionary processes that shape organelle genomes in Apiaceae, with implications for broader plant genome evolution.},
}

*Genome, Mitochondrial
*Genome, Plastid
*Cell Nucleus/genetics
*Apiaceae/genetics
Phylogeny
Evolution, Molecular
Genome, Plant
DNA, Plant/genetics
Plastids/genetics

@article {pmid39893444,
year = {2025},
author = {Hao, J and Liang, Y and Wang, T and Su, Y},
title = {Correlations of gene expression, codon usage bias, and evolutionary rates of the mitochondrial genome show tissue differentiation in Ophioglossum vulgatum.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {134},
pmid = {39893444},
issn = {1471-2229},
support = {31872670//National Natural Science Foundation of China/ ; 32071781//National Natural Science Foundation of China/ ; },
mesh = {*Genome, Mitochondrial ; *Codon Usage ; *Evolution, Molecular ; Gene Expression Regulation, Plant ; Transcriptome ; Codon/genetics ; Plant Leaves/genetics ; },
abstract = {BACKGROUND: Mitochondria are crucial for energy production in plant tissues, but their quantity and activity vary in different tissues and developmental processes. Determining the factors underlying differential molecular evolutionary rates has long been a central question in evolutionary biology, with expression level emerging as the prime predictor. Although we have previously observed an anti-correlation between expression level (E) and evolutionary rate (R) in chloroplast genes, it remains unclear whether such an anti-correlation exists in plant mitochondrial genes. Ophioglossum vulgatum is a typical plant belonging to the Ophioglossaceae, characterized by its unique morphology with only a single leaf above ground. It holds significant scientific and medicinal value. Using the mitochondrial genome and transcriptome data of O. vulgatum, we first analyzed the correlation between mitochondrial gene expression, codon usage bias, and evolutionary rates in different tissues.

RESULTS: Our findings indicated that mitochondrial gene expression level was the strongest between stem and leaf, while the weakest was between sporangium and root. Kruskal-Wallis tests revealed significant differences across various tissue types. Codon usage bias was influenced by both mutation and selection, with selection exerting a greater impact. The Spearman's rank correlation coefficients between codon adaptation index and expression levels of sporangium, stem, leaf, and root were 0.1178, 0.3926, 0.4463, and 0.2945, respectively, with significance in stem and leaf (P < 0.05). The correlation coefficients between the nonsynonymous substitution rate (dN) and expression levels in sporangium, stem, leaf, and root were -0.0840, -0.1786, -0.1714, and -0.0857, respectively, yet none are statistically significant. The correlation coefficient between the synonymous substitution rate (dS) and expression levels in sporangium was negative, whereas those between dS and the stem, leaf, and root were positive, although they were not significant. The dN/dS ratio exhibited a significant negative correlation with expression levels in both leaf and root (P < 0.05).

CONCLUSIONS: For the first time, our study revealed differences in the correlation between mitochondrial gene expression and codon usage bias, as well as evolutionary rates, across various tissues of O. vulgatum. Moreover, we also provide novel insights into understanding the effects of plant mitochondrial gene expression on evolutionary patterns.},
}

*Genome, Mitochondrial
*Codon Usage
*Evolution, Molecular
Gene Expression Regulation, Plant
Transcriptome
Codon/genetics
Plant Leaves/genetics

@article {pmid39892694,
year = {2025},
author = {Uzoigwe, CE},
title = {Nuclear Quantum Effects Explain Chemiosmosis: The Power of the Proton.},
journal = {Bio Systems},
volume = {},
number = {},
pages = {105407},
doi = {10.1016/j.biosystems.2025.105407},
pmid = {39892694},
issn = {1872-8324},
abstract = {ATP is a universal bio-currency, with chemiosmosis the metabolic mint by which currency is printed. Chemiosmosis leverages a membrane potential and ion gradient, typically a proton gradient, to generate ATP. The current chemiosmotic hypothesis is both cannon and dogma. However, there are obstacles to the unqualified and uncritical acceptance of this model. Intriguingly the proton is sufficiently small to exhibit quantum phenomena of wave-particle duality, often thought the exclusive prerogative of smaller subcellular particles. Evidence shows that chemiosmosis is by necessity critically dependent upon these nuclear quantum effects (NQE) of hydrogen, most notably as a proton. It is well established scientific orthodoxy that protons in water and hydrogen atoms of water molecules exhibit quantum phenomena. The effect is amplified by the hydrogen bonding and juxta-membrane location of protons in mitochondria and chloroplasts. NQE explains the otherwise inexplicable features of chemiosmosis, including the paucity of protons, the rate of the proton movement and ATP genesis in otherwise subliminal proton motive forces and thus functionality of alkaliphiles. It also accounts for the efficiencies of chemiosmosis reported at greater than 100% in certain contexts, which violates the second law of thermodynamics under the paradigm of classical physics. Mitochondria may have evolved to exploit quantum biology with notable features such as dimeric ATP synthases adumbrating the first double-slip experiment with the protons. The dramatic global deceleration of mitochondrial chemiosmosis and all cellular function following proton substitution with is heavier isotopes, deuterium and tritium: "deuteruction", is testimony to the primacy of nuclear quantum effects in this Quantum Chemiosmosis. Indeed the speed of evolution itself and its inexorable route to homeothermy may be due to the power of nuclear quantum effects of the smallest nucleus, the proton. The atom that is almost nothing was selected to bring about the most important processes and complex manifestations of life.},
}

@article {pmid39888573,
year = {2025},
author = {Brzezniakiewicz-Janus, K and Jarczak, J and Konopko, A and Ratajczak, J and Kucia, M and Ratajczak, MZ},
title = {Mitochondria Express Functional Signaling Ligand-Binding Receptors that Regulate their Biological Responses - the Novel Role of Mitochondria as Stress-Response Sentinels.},
journal = {Stem cell reviews and reports},
volume = {},
number = {},
pages = {},
pmid = {39888573},
issn = {2629-3277},
support = {UMO-2022/45/B/NZ6/00475//Narodowe Centrum Nauki/ ; },
abstract = {Evidence accumulated mitochondria, as the "powerplants of the cell," express several functional receptors for external ligands that modify their function and regulate cell biology. This review sheds new light on the role of these organelles in sensing external stimuli to facilitate energy production for cellular needs. This is possible because mitochondria express some receptors on their membranes that are responsible for their autonomous responses. This is not surprising given the widely accepted hypothesis that these intracellular organelles originated from prokaryotic ancestors that fused with eukaryotic cells during early evolution. It has been reported that mitochondria express functional estrogen, androgen, glucocorticoid, 5-hydroxytryptamine, melatonin, and cannabinoid receptors. What is intriguing is recent evidence showing that mitochondria could also be directly regulated by active mediators of intracellular complement (complosome) and intrinsic mediators of purinergic signaling. Accordingly, they express receptors for intracellular complement cleavage fragments (C5a and C3a) as well as for adenosine triphosphate (ATP), which, besides its crucial role in transferring energy in the cells, is also an important signaling molecule interacting with P2X7 receptor expressed not only on the cell surface but also on the mitochondria membrane. Based on this, intrinsic complosome and purinergic signaling mediators emerge as important cooperating regulators of reactive oxygen species (ROS) release from mitochondria and activators of intracellular pattern recognition receptor Nlrp3 inflammasome. This activation within the beneficial "hormetic zone response" regulates cell metabolism, proliferation, migration, and adaptation to the surrounding challenges of the microenvironment in a favorable way.},
}

@article {pmid39878681,
year = {2025},
author = {Zhao, K and Zhang, H and Ding, W and Yu, X and Hou, Y and Liu, X and Li, X and Wang, X},
title = {Adipokines regulate the development and progression of MASLD through organellar oxidative stress.},
journal = {Hepatology communications},
volume = {9},
number = {2},
pages = {},
pmid = {39878681},
issn = {2471-254X},
mesh = {Humans ; *Oxidative Stress/physiology ; *Adipokines/metabolism ; *Disease Progression ; Fatty Liver/metabolism/physiopathology ; Endoplasmic Reticulum Stress/physiology ; Mitochondria/metabolism ; Reactive Oxygen Species/metabolism ; Animals ; },
abstract = {The prevalence of metabolic dysfunction-associated steatotic liver disease (MASLD), which is increasingly being recognized as a leading cause of chronic liver pathology globally, is increasing. The pathophysiological underpinnings of its progression, which is currently under active investigation, involve oxidative stress. Human adipose tissue, an integral endocrine organ, secretes an array of adipokines that are modulated by dietary patterns and lifestyle choices. These adipokines intricately orchestrate regulatory pathways that impact glucose and lipid metabolism, oxidative stress, and mitochondrial function, thereby influencing the evolution of hepatic steatosis and progression to metabolic dysfunction-associated steatohepatitis (MASH). This review examines recent data, underscoring the critical interplay of oxidative stress, reactive oxygen species, and redox signaling in adipokine-mediated mechanisms. The role of various adipokines in regulating the onset and progression of MASLD/MASH through mitochondrial dysfunction and endoplasmic reticulum stress and the underlying mechanisms are discussed. Due to the emerging correlation between adipokines and the development of MASLD positions, these adipokines are potential targets for the development of innovative therapeutic interventions for MASLD management. A comprehensive understanding of the pathogenesis of MASLD/MASH is instrumental for identifying therapies for MASH.},
}

Humans
*Oxidative Stress/physiology
*Adipokines/metabolism
*Disease Progression
Fatty Liver/metabolism/physiopathology
Endoplasmic Reticulum Stress/physiology
Mitochondria/metabolism
Reactive Oxygen Species/metabolism
Animals

@article {pmid39871928,
year = {2022},
author = {Li, J and Cui, J and Tian, Y},
title = {Neuron-periphery mitochondrial stress communication in aging and diseases.},
journal = {Life medicine},
volume = {1},
number = {2},
pages = {168-178},
pmid = {39871928},
issn = {2755-1733},
abstract = {The nervous system is the central hub of the body, detecting environmental and internal stimuli to regulate organismal metabolism via communications to the peripheral tissues. Mitochondria play an essential role in neuronal activity by supplying energy, maintaining cellular metabolism, and buffering calcium levels. A variety of mitochondrial conditions are associated with aging and age-related neurological disorders. Beyond regulating individual neuron cells, mitochondria also coordinate signaling in tissues and organs during stress conditions to mediate systemic metabolism and enable organisms to adapt to such stresses. In addition, peripheral organs and immune cells can also produce signaling molecules to modulate neuronal function. Recent studies have found that mitokines released upon mitochondrial stresses affect metabolism and the physiology of different tissues and organs at a distance. Here, we summarize recent advances in understanding neuron-periphery mitochondrial stress communication and how mitokine signals contribute to the systemic regulation of metabolism and aging with potential implications for therapeutic strategies.},
}

@article {pmid39870744,
year = {2025},
author = {Tan, I and Chothani, S and Lim, HH and Lam, KP},
title = {Alu-Sc-mediated exonization generated a mitochondrial LKB1 gene variant found only in higher order primates.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {3360},
pmid = {39870744},
issn = {2045-2322},
mesh = {Animals ; Humans ; *Exons/genetics ; *Alu Elements/genetics ; *Protein Serine-Threonine Kinases/genetics ; *Primates/genetics ; AMP-Activated Protein Kinase Kinases ; Mitochondria/genetics ; Alternative Splicing ; Evolution, Molecular ; },
abstract = {The tumor suppressor LKB1/STK11 plays important roles in regulating cellular metabolism and stress responses and its mutations are associated with various cancers. We recently identified a novel exon 1b within intron 1 of human LKB1/STK11, which generates an alternatively spliced, mitochondria-targeting LKB1 isoform important for regulating mitochondrial oxidative stress. Here we examined the formation of this novel exon 1b and uncovered its relatively late emergence during evolution. Analyses of putative exon 1b genomic sequences within the primate superfamily indicated that the exonization of LKB1/STK11 exon 1b was mediated by the conserved retrotransposable element Alu-Sc. While putative exon 1b sequences are recognizable in most members of the primate family from New World Monkeys onwards, characteristically functional LKB1/STK11 exon 1b, with translation start and 5' and 3' splice sites, could only be found in greater apes and human, and interestingly, correlates with their increased body mass and longevity development.},
}

Animals
Humans
*Exons/genetics
*Alu Elements/genetics
*Protein Serine-Threonine Kinases/genetics
*Primates/genetics
AMP-Activated Protein Kinase Kinases
Mitochondria/genetics
Alternative Splicing
Evolution, Molecular

@article {pmid39863913,
year = {2025},
author = {Komza, M and Khatun, J and Gelles, JD and Trotta, AP and Abraham-Enachescu, I and Henao, J and Elsaadi, A and Kotini, AG and Clementelli, C and Arandela, J and Ghaity-Beckley, SE and Barua, A and Chen, Y and Berisa, M and Marcellino, BK and Papapetrou, EP and Poyurovsky, MV and Chipuk, JE},
title = {Metabolic adaptations to acute glucose uptake inhibition converge upon mitochondrial respiration for leukemia cell survival.},
journal = {Cell communication and signaling : CCS},
volume = {23},
number = {1},
pages = {47},
pmid = {39863913},
issn = {1478-811X},
mesh = {Humans ; *Mitochondria/metabolism/drug effects ; *Glucose/metabolism ; *Cell Survival/drug effects ; Leukemia, Myeloid, Acute/pathology/metabolism/genetics/drug therapy ; Cell Respiration/drug effects ; Glycolysis/drug effects ; Oxidative Phosphorylation/drug effects ; Cell Line, Tumor ; Adaptation, Physiological ; },
abstract = {One hallmark of cancer is the upregulation and dependency on glucose metabolism to fuel macromolecule biosynthesis and rapid proliferation. Despite significant pre-clinical effort to exploit this pathway, additional mechanistic insights are necessary to prioritize the diversity of metabolic adaptations upon acute loss of glucose metabolism. Here, we investigated a potent small molecule inhibitor to Class I glucose transporters, KL-11743, using glycolytic leukemia cell lines and patient-based model systems. Our results reveal that while several metabolic adaptations occur in response to acute glucose uptake inhibition, the most critical is increased mitochondrial oxidative phosphorylation. KL-11743 treatment efficiently blocks the majority of glucose uptake and glycolysis, yet markedly increases mitochondrial respiration via enhanced Complex I function. Compared to partial glucose uptake inhibition, dependency on mitochondrial respiration is less apparent suggesting robust blockage of glucose uptake is essential to create a metabolic vulnerability. When wild-type and oncogenic RAS patient-derived induced pluripotent stem cell acute myeloid leukemia (AML) models were examined, KL-11743 mediated induction of mitochondrial respiration and dependency for survival associated with oncogenic RAS. Furthermore, we examined the therapeutic potential of these observations by treating a cohort of primary AML patient samples with KL-11743 and witnessed similar dependency on mitochondrial respiration for sustained cellular survival. Together, these data highlight conserved adaptations to acute glucose uptake inhibition in diverse leukemic models and AML patient samples, and position mitochondrial respiration as a key determinant of treatment success.},
}

Humans
*Mitochondria/metabolism/drug effects
*Glucose/metabolism
*Cell Survival/drug effects
Leukemia, Myeloid, Acute/pathology/metabolism/genetics/drug therapy
Cell Respiration/drug effects
Glycolysis/drug effects
Oxidative Phosphorylation/drug effects
Cell Line, Tumor
Adaptation, Physiological

@article {pmid39860980,
year = {2024},
author = {Han, L and Yang, Y and Lu, M and Yu, H and Lu, Y and Zhou, M and Liu, T and Zhang, R and Chen, B and Hou, Z},
title = {Mitogenome Phylogenetics of Spiruromorpha Porpoise Parasite: Insights Into Phylogeny of Crassicauda magna.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {1},
pages = {},
pmid = {39860980},
issn = {2076-0817},
support = {415471//the Postdoctoral Funding Program of Heilongjiang Province, China/ ; GZC20230394//the State-sponsored Postdoctoral Researcher program/ ; },
mesh = {*Phylogeny ; *Genome, Mitochondrial/genetics ; Animals ; Porpoises/genetics/parasitology ; },
abstract = {(1) Background: Crassicauda magna is a major parasite of large porpoises and whales and has been classified in the Habronematoidea family. However, there has been a great controversy regarding its classification. Mitochondria have an important function in revealing taxonomic and evolutionary history. (2) Methods: In this study, we sequenced the mitochondrial genome of C. magna and conducted a phylogenetic analysis with the mitochondrial sequences of species belonging to the Habronematoidea family. (3) Results: The complete mitochondrial genome was 13,604 bp and it has an AT-rich sequence and one non-coding region (NCR). The reconstruction of the ancestral state showed that the gene orders of all species in Spirurina were conserved. The phylogenetic tree indicates that C. magna is closer to Heliconema longissimum (Physalopteroidea) than Tetrameres grusi (Habronematoidea). (4) Conclusions: This study provides new evidence that C. magna is phylogenetically closer to Physalopteroidea at the molecular taxonomic level.},
}

*Phylogeny
*Genome, Mitochondrial/genetics
Animals
Porpoises/genetics/parasitology

@article {pmid39859262,
year = {2025},
author = {Cui, J and Yang, Q and Zhang, J and Ju, C and Cui, S},
title = {Mitochondrial Genome Insights into Evolution and Gene Regulation in Phragmites australis.},
journal = {International journal of molecular sciences},
volume = {26},
number = {2},
pages = {},
doi = {10.3390/ijms26020546},
pmid = {39859262},
issn = {1422-0067},
support = {31170784, 31972934//National Natural Science Foundation of China/ ; 19530050183//special fund from Capital Normal University/ ; },
mesh = {*Genome, Mitochondrial ; *Poaceae/genetics ; *Evolution, Molecular ; *Phylogeny ; Gene Expression Regulation, Plant ; RNA Editing ; Molecular Sequence Annotation ; Genome, Plant ; },
abstract = {As a globally distributed perennial Gramineae, Phragmites australis can adapt to harsh ecological environments and has significant economic and environmental values. Here, we performed a complete assembly and annotation of the mitogenome of P. australis using genomic data from the PacBio and BGI platforms. The P. australis mitogenome is a multibranched structure of 501,134 bp, divided into two circular chromosomes of 325,493 bp and 175,641 bp, respectively. A sequence-simplified succinate dehydrogenase 4 gene was identified in this mitogenome, which is often translocated to the nuclear genome in the mitogenomes of gramineous species. We also identified tissue-specific mitochondrial differentially expressed genes using RNAseq data, providing new insights into understanding energy allocation and gene regulatory strategies in the long-term adaptive evolution of P. australis mitochondria. In addition, we studied the mitogenome features of P. australis in more detail, including repetitive sequences, gene Ka/Ks analyses, codon preferences, intracellular gene transfer, RNA editing, and multispecies phylogenetic analyses. Our results provide an essential molecular resource for understanding the genetic characterisation of the mitogenome of P. australis and provide a research basis for population genetics and species evolution in Arundiaceae.},
}

*Genome, Mitochondrial
*Poaceae/genetics
*Evolution, Molecular
*Phylogeny
Gene Expression Regulation, Plant
RNA Editing
Molecular Sequence Annotation
Genome, Plant

@article {pmid39848024,
year = {2025},
author = {Gureev, AP and Nesterova, VV and Sadovnikova, IS},
title = {Long-range PCR as a tool for evaluating mitochondrial DNA damage: Principles, benefits, and limitations of the technique.},
journal = {DNA repair},
volume = {146},
number = {},
pages = {103812},
doi = {10.1016/j.dnarep.2025.103812},
pmid = {39848024},
issn = {1568-7856},
abstract = {Mitochondrial DNA (mtDNA) is often more susceptible to damage compared to nuclear DNA. This is due to its localization in the mitochondrial matrix, where a large portion of reactive oxygen species are produced. Mitochondria do not have histones and mtDNA is only slightly protected by histone-like proteins and is believed to have less efficient repair mechanisms. In this review, we discuss the long-range PCR method, which allows for the effective detection of mtDNA damage. The method is based on the assumption that various types of DNA lesions can interfere the progress of DNA polymerase, resulting in reduced amplification efficiency. It can be used to estimate the number of additional (above background) lesions in mtDNA. The review outlines the evolution of the methodology, its variations, applications in a wide range of model organisms, the advantages of the method and its limitations, as well as ways to overcome these limitations. Over the past two decades, the use of long-range PCR has allowed the study of mtDNA repair mechanisms, the characteristics of mitochondrial genome damage in various neurodegenerative diseases, aging, ischemic and oncological processes, as well as in anticancer therapy. The assessment of mtDNA damage has also been proposed for use in environmental biomonitoring. This review provides a critical evaluation of the various variations of this method, summarizes the accumulated data, and discusses the role of mtDNA damage in different organs at the organismal level.},
}

@article {pmid39847522,
year = {2025},
author = {Weinstein, B and Wang, Z and Zhou, Q and Roy, SW},
title = {ZW sex chromosome differentiation in paleognathous birds is associated with mitochondrial effective population size but not mitochondrial genome size or mutation rate.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evaf005},
pmid = {39847522},
issn = {1759-6653},
abstract = {Eukaryotic genome size varies considerably, even among closely related species. The causes of this variation are unclear, but weak selection against supposedly costly "extra" genomic sequences has been central to the debate for over 50 years. The mutational hazard hypothesis, which focuses on the increased mutation rate to null alleles in superfluous sequences, is particularly influential, though challenging to test. This study examines the sex chromosomes and mitochondrial genomes of 15 flightless or semi-flighted paleognathous bird species. In this clade, the non-recombining portion of the W chromosome has independently expanded stepwise in multiple lineages. Given the shared maternal inheritance of the W chromosome and mitochondria, theory predicts that mitochondrial effective population size (Ne) should decrease due to increased Hill-Robertson Interference in lineages with expanded non-recombining W regions. Our findings support the extent of the non-recombining W region with three indicators of reduced selective efficiency: (1) the ratio of non-synonymous to synonymous nucleotide changes in the mitochondrion, (2) the probability of radical amino acid changes, and (3) the number of ancient, W-linked genes lost through evolution. Next, we tested whether reduced Ne affects mitochondrial genome size, as predicted by weak selection against genome expansion. We find no support for a relationship between mitochondrial genome size and expanded non-recombining W regions, nor with increased mitochondrial mutation rates (predicted to modulate selective costs). These results highlight the utility of non-recombining regions and mitochondrial genomes for studying genome evolution and challenge the general idea of a negative relation between the efficacy of selection and genome size.},
}

@article {pmid39847448,
year = {2025},
author = {Wang, S and Luo, H},
title = {Dating the bacterial tree of life based on ancient symbiosis.},
journal = {Systematic biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/sysbio/syae071},
pmid = {39847448},
issn = {1076-836X},
abstract = {Obtaining a timescale for bacterial evolution is crucial to understand early life evolution but is difficult owing to the scarcity of bacterial fossils. Here, we introduce multiple new time constraints to calibrate bacterial evolution based on ancient symbiosis. This idea is implemented using a bacterial tree constructed with genes found in the mitochondrial lineages phylogenetically embedded within Proteobacteria. The expanded mitochondria-bacterial tree allows the node age constraints of eukaryotes established by their abundant fossils to be propagated to ancient co-evolving bacterial symbionts and across the bacterial tree of life. Importantly, we formulate a new probabilistic framework that considers uncertainty in inference of the ancestral lifestyle of modern symbionts to apply 19 relative time constraints (RTC) each informed by host-symbiont association to constrain bacterial symbionts no older than their eukaryotic host. Moreover, we develop an approach to incorporating substitution mixture models that better accommodate substitutional saturation and compositional heterogeneity for dating deep phylogenies. Our analysis estimates that the last bacterial common ancestor (LBCA) occurred approximately 4.0-3.5 billion years ago (Ga), followed by rapid divergence of major bacterial clades. It is generally robust to alternative root ages, root positions, tree topologies, fossil ages, ancestral lifestyle reconstruction, gene sets, among other factors. The obtained timetree serves as a foundation for testing hypotheses regarding bacterial diversification and its correlation with geobiological events across different timescales.},
}

@article {pmid39833664,
year = {2025},
author = {Tan, S and Wang, W and Li, J and Sha, Z},
title = {Comprehensive analysis of 111 Pleuronectiformes mitochondrial genomes: insights into structure, conservation, variation and evolution.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {50},
pmid = {39833664},
issn = {1471-2164},
mesh = {*Genome, Mitochondrial ; Animals ; *Flatfishes/genetics ; *Phylogeny ; *Evolution, Molecular ; Genetic Variation ; RNA, Transfer/genetics ; Codon Usage ; Gene Rearrangement ; Genomics/methods ; },
abstract = {BACKGROUND: Pleuronectiformes, also known as flatfish, are important model and economic animals. However, a comprehensive genome survey of their important organelles, mitochondria, has been limited. Therefore, we aim to analyze the genomic structure, codon preference, nucleotide diversity, selective pressure and repeat sequences, as well as reconstruct the phylogenetic relationship using the mitochondrial genomes of 111 flatfish species.

RESULTS: Our analysis revealed a conserved gene content of protein-coding genes and rRNA genes, but varying numbers of tRNA genes and control regions across species. Various gene rearrangements were found in flatfish species, especially for the rearrangement of nad5-nad6-cytb block in Samaridae family, the swapping rearrangement of nad6 and cytb gene in Bothidae family, as well as the control region translocation and tRNA-Gln gene inversion in the subfamily Cynoglossinae, suggesting their unique evolutionary history and/or functional benefit. Codon usage showed obvious biases, with adenine being the most frequent nucleotide at the third codon position. Nucleotide diversity and selective pressure analysis suggested that different protein-coding genes underwent varying degrees of evolutionary pressure, with cytb and cox genes being the most conserved ones. Phylogenetic analysis using both whole mitogenome information and concatenated independently aligned protein-coding genes largely mirrored the taxonomic classification of the species, but showed different phylogeny. The identification of simple sequence repeats and various long repetitive sequences provided additional complexity of genome organization and offered markers for evolutionary studies and breeding practices.

CONCLUSIONS: This study represents a significant step forward in our comprehension of the flatfish mitochondrial genomes, providing valuable insights into the structure, conservation and variation within flatfish mitogenomes, with implications for understanding their evolutionary history, functional genomics and fisheries management. Future research can delve deeper into conservation biology, evolutionary biology and functional usages of variations.},
}

*Genome, Mitochondrial
Animals
*Flatfishes/genetics
*Phylogeny
*Evolution, Molecular
Genetic Variation
RNA, Transfer/genetics
Codon Usage
Gene Rearrangement
Genomics/methods

@article {pmid39819387,
year = {2025},
author = {Li, H and Liu, L and Qiu, Z and He, F and Dong, W},
title = {Complete mitochondrial genome assembly and comparative analysis of Colocasia esculenta.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {67},
pmid = {39819387},
issn = {1471-2229},
support = {2021GXNSFBA196012, 2022GXNSFAA035493//Natural Science Foundation of Guangxi/ ; TS202113//the Lipu C. esculenta Test Station Project of Guangxi/ ; Gui nongke 2023YM91, Gui nongke 2024YP081//Basic Scientific Research Business Project of Guangxi Academy of Agricultural Sciences/ ; },
mesh = {*Genome, Mitochondrial ; *Colocasia/genetics ; *Phylogeny ; Genome, Plant ; Base Composition ; },
abstract = {Colocasia esculenta ranks as the fifth most important tuber crop and is known for its high nutritional and medicinal value. However, there is no research on its mitochondrial genome, hindering in-depth exploration of its genomic resources and genetic relationships. Using second- and third-generation sequencing technologies, we assembled and annotated the mitogenome of C. esculenta. Its mitogenome mainly consists of five circular DNA molecules, with a total length of 594,811 bp and a GC content of 46.25%. A total of 55 genes, 157 simple sequence repeats, 29 tandem repeat sequences, 202 dispersed repeat sequences, and 625 RNA editing sites were detected. Most protein-coding genes use ATG as the start codon, and the third position of the codon tends to be A or T (U). GAA, AUU, and UUU are the most common codons in C. esculenta mitochondria. Finally, based on 28 representative plant species, a phylogenetic tree was constructed, revealing a close relationship between C. esculenta and Araceae. This study provides comprehensive information on C. esculenta, laying a foundation for crop genetics and molecular breeding.},
}

*Genome, Mitochondrial
*Colocasia/genetics
*Phylogeny
Genome, Plant
Base Composition

@article {pmid39806272,
year = {2025},
author = {Mazzocca, A and Ferraro, G and Misciagna, G},
title = {The systemic evolutionary theory of the origin of cancer (SETOC): an update.},
journal = {Molecular medicine (Cambridge, Mass.)},
volume = {31},
number = {1},
pages = {12},
pmid = {39806272},
issn = {1528-3658},
mesh = {Humans ; *Neoplasms/metabolism/pathology/genetics ; *Biological Evolution ; Animals ; Cell Transformation, Neoplastic/genetics/metabolism ; Tumor Microenvironment ; },
abstract = {The Systemic Evolutionary Theory of the Origin of Cancer (SETOC) is a recently proposed theory founded on two primary principles: the cooperative and endosymbiotic process of cell evolution as described by Lynn Margulis, and the integration of complex systems operating in eukaryotic cells, which is a core concept in systems biology. The SETOC proposes that malignant transformation occurs when cells undergo a continuous adaptation process in response to long-term injuries, leading to tissue remodeling, chronic inflammation, fibrosis, and ultimately cancer. This process involves a maladaptive response, wherein the 'endosymbiotic contract' between the nuclear-cytoplasmic system (derived from the primordial archaeal cell) and the mitochondrial system (derived from the primordial α-proteobacterium) gradually breaks down. This ultimately leads to uncoordinated behaviors and functions in transformed cells. The decoupling of the two cellular subsystems causes transformed cells to acquire phenotypic characteristics analogous to those of unicellular organisms, as well as certain biological features of embryonic development that are normally suppressed. These adaptive changes enable cancer cells to survive in the harsh tumor microenvironment characterized by low oxygen concentrations, inadequate nutrients, increased catabolic waste, and increased acidity. De-endosymbiosis reprograms the sequential metabolic functions of glycolysis, the TCA cycle, and oxidative phosphorylation (OxPhos). This leads to increased lactate fermentation (Warburg effect), respiratory chain dysfunction, and TCA cycle reversal. Here, we present an updated version of the SETOC that incorporates the fundamental principles outlined by this theory and integrates the epistemological approach used to develop it.},
}

Humans
*Neoplasms/metabolism/pathology/genetics
*Biological Evolution
Animals
Cell Transformation, Neoplastic/genetics/metabolism
Tumor Microenvironment

@article {pmid39804925,
year = {2025},
author = {Ricou, A and Simon, M and Duflos, R and Azzopardi, M and Roux, F and Budar, F and Camilleri, C},
title = {Identification of novel genes responsible for a pollen killer present in local natural populations of Arabidopsis thaliana.},
journal = {PLoS genetics},
volume = {21},
number = {1},
pages = {e1011451},
doi = {10.1371/journal.pgen.1011451},
pmid = {39804925},
issn = {1553-7404},
abstract = {Gamete killers are genetic loci that distort segregation in the progeny of hybrids because the killer allele promotes the elimination of the gametes that carry the sensitive allele. They are widely distributed in eukaryotes and are important for understanding genome evolution and speciation. We had previously identified a pollen killer in hybrids between two distant natural accessions of Arabidopsis thaliana. This pollen killer involves three genetically linked genes, and we previously reported the identification of the gene encoding the antidote that protects pollen grains from the killer activity. In this study, we identified the two other genes of the pollen killer by using CRISPR-Cas9 induced mutants. These two genes are necessary for the killer activity that we demonstrated to be specific to pollen. The cellular localization of the pollen killer encoded proteins suggests that the pollen killer activity involves the mitochondria. Sequence analyses reveal predicted domains from the same families in the killer proteins. In addition, the C-terminal half of one of the killer proteins is identical to the antidote, and one amino acid, crucial for the antidote activity, is also essential for the killer function. Investigating more than 700 worldwide accessions of A. thaliana, we confirmed that the locus is subject to important structural rearrangements and copy number variation. By exploiting available de novo genomic sequences, we propose a scenario for the emergence of this pollen killer in A. thaliana. Furthermore, we report the co-occurrence and behavior of killer and sensitive genotypes in several local populations, a prerequisite for studying gamete killer evolution in the wild. This highlights the potential of the Arabidopsis model not only for functional studies of gamete killers but also for investigating their evolutionary trajectories at complementary geographical scales.},
}

@article {pmid39799216,
year = {2025},
author = {Shi, C and Guo, Y and Yao, L and Xu, Y and Zhou, J and Hua, M},
title = {Development of a mitochondrial mini-barcode and its application in metabarcoding for identification of leech in traditional Chinese medicine.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {1698},
pmid = {39799216},
issn = {2045-2322},
mesh = {Animals ; *Leeches/genetics ; *DNA Barcoding, Taxonomic/methods ; *Medicine, Chinese Traditional ; RNA, Ribosomal, 16S/genetics ; Genome, Mitochondrial ; DNA, Mitochondrial/genetics ; Mitochondria/genetics ; Phylogeny ; },
abstract = {In Traditional Chinese Medicine (TCM), the medicinal leech is vital for treatments to promote blood circulation and eliminate blood stasis. However, the prevalence of counterfeit leech products in the market undermines the quality and efficacy of these remedies. Traditional DNA barcoding techniques, such as the COI barcode, have been limited in their application due to amplification challenges. This study identified high variability in the 16 S rRNA gene within the mitochondrial genome across five leech species, leading to the development of a novel 219 bp mini-barcode. Compared with the traditional COI barcode, our mini-barcode showed remarkable identification efficiency, classifying 142 out of 147 leech samples from fresh and processed materials. In contrast, the COI barcode could only successfully identify 79 out of the 147 samples. In the case of seven batches of leech decoction pieces, the mini-barcode identified six, whereas the COI barcode only recognized one. Additionally, the mini-barcode effectively discerned five leech species within Chinese patent medicines when combined with metabarcoding technology. These results confirm the mini-barcode's potential as a reliable tool for rapidly and precisely identifying leech species in TCM products.},
}

Animals
*Leeches/genetics
*DNA Barcoding, Taxonomic/methods
*Medicine, Chinese Traditional
RNA, Ribosomal, 16S/genetics
Genome, Mitochondrial
DNA, Mitochondrial/genetics
Mitochondria/genetics
Phylogeny

@article {pmid39796122,
year = {2024},
author = {Queiroz, ALF and Garcia, CB and Silva, JPMO and Cavalini, DFA and Alexandrino, AV and Cunha, AF and Vercesi, AE and Castilho, RF and Shiguemoto, GE},
title = {Preventive Effects of Resistance Training on Hemodynamics and Kidney Mitochondrial Bioenergetic Function in Ovariectomized Rats.},
journal = {International journal of molecular sciences},
volume = {26},
number = {1},
pages = {},
pmid = {39796122},
issn = {1422-0067},
mesh = {Animals ; *Ovariectomy ; Female ; *Kidney/metabolism ; *Hemodynamics ; *Mitochondria/metabolism ; Rats ; *Rats, Wistar ; *Energy Metabolism ; *Resistance Training/methods ; *Physical Conditioning, Animal ; Oxidative Phosphorylation ; },
abstract = {Menopause occurs due to the depletion of the ovarian reserve, leading to a progressive decline in estrogen (E2) levels. This decrease in E2 levels increases the risk of developing several diseases and can coexist with chronic kidney disease (CKD). Arterial hypertension (AH) is another condition associated with menopause and may either contribute to or result from CKD. Ovariectomy (OVX) induces hypoestrogenism, which can lead to mitochondrial bioenergetic dysfunction in the kidneys. Previous studies have suggested that exercise training has beneficial effects on adults with CKD and AH. To investigate the effects of OVX and resistance training (RT) on hemodynamic parameters and mitochondrial bioenergetic function of the kidney, female Wistar rats were divided into ovariectomized (OVX) and intact (INT) groups. These rats were either kept sedentary (SED) or subjected to RT for thirteen weeks. The RT involved climbing a vertical ladder with a workload apparatus. Hemodynamic parameters were assessed via tail plethysmography. Mitochondrial respiratory function was evaluated with high-resolution respirometry. Gene expression related to the electron transport chain (ETC) and oxidative phosphorylation (OXPHOS) was evaluated by real-time qPCR. At week 13, key hemodynamic parameters (systolic blood pressure and mean arterial pressure) were significantly elevated in the OVX-SED group. Compared with those in the other groups, mitochondrial bioenergetics were impaired in the OVX-SED group. In contrast, the trained groups presented improved mitochondrial bioenergetic function compared with the sedentary groups. OVX led to reduced gene expression related to the mitochondrial ETC and OXPHOS, whereas RT both prevented this reduction and increased gene expression in the trained groups. Our results indicate that hypoestrogenism significantly decreases OXPHOS and ETC capacity in the kidneys of sedentary animals. However, RT effectively increased the expression of genes related to mitochondrial ETC and OXPHOS, thereby counteracting the effects of OVX.},
}

Animals
*Ovariectomy
Female
*Kidney/metabolism
*Hemodynamics
*Mitochondria/metabolism
Rats
*Rats, Wistar
*Energy Metabolism
*Resistance Training/methods
*Physical Conditioning, Animal
Oxidative Phosphorylation

@article {pmid39775223,
year = {2025},
author = {de Oliveira, EC and Tibúrcio, R and Duarte, G and Lago, A and de Melo, L and Nunes, S and Davanzo, GG and Martins, AJ and Ribeiro, BV and Mothé, D and Menezes, JBP and Veras, P and Tavares, N and Moraes-Vieira, PM and Brodskyn, CI},
title = {Pharmacological inhibition of key metabolic pathways attenuates Leishmania spp infection in macrophages.},
journal = {PLoS neglected tropical diseases},
volume = {19},
number = {1},
pages = {e0012763},
doi = {10.1371/journal.pntd.0012763},
pmid = {39775223},
issn = {1935-2735},
abstract = {Macrophages represent a fundamental component of the innate immune system that play a critical role in detecting and responding to pathogens as well as danger signals. Leishmania spp. infections lead to a notable alteration in macrophage metabolism, whereby infected cells display heightened energy metabolism that is linked to the integrity of host mitochondria. However, little is known about how different species of Leishmania manipulate host metabolism. Here, we demonstrate that despite differences in their mechanisms for evading host immune responses, L. amazonensis and L. braziliensis induce comparable disruptions in key metabolic pathways. We found that infected macrophages exhibited an overall elevation in energy metabolism regardless of the parasite strain, evidenced by the elevation in glycolysis and oxygen consumption rates, along with increased proton leak and decreased ATP production. We also analyzed the effects of both Leishmania spp. strain infection on mitochondria function, further revealing that infected cells display heightened mitochondrial mass and membrane potential. To investigate the metabolic pathways required for Leishmania amastigotes to persist in BMDMs, we pre-treated cells with small molecule drugs that target major metabolic pathways, revealing that perturbations in several metabolic processes affected parasite survival in a strain-independent manner. Treatments with inhibitors of the oxidative phosphorylation and glycolysis substantially reduced parasite loads. Collectively, our findings suggest that L.amazonensis and L.braziliensis exploit host cell metabolic pathways similarly to survive in macrophages.},
}

@article {pmid39662740,
year = {2025},
author = {de Quadros, T and Jaramillo, ML and Barreto, C and da Rosa, RD and de Melo, MS and Nazari, EM},
title = {Modulation of mitochondrial dynamics genes and mtDNA during embryonic development and under UVB exposure.},
journal = {Comparative biochemistry and physiology. Part A, Molecular & integrative physiology},
volume = {300},
number = {},
pages = {111790},
doi = {10.1016/j.cbpa.2024.111790},
pmid = {39662740},
issn = {1531-4332},
mesh = {Animals ; *Ultraviolet Rays ; *DNA, Mitochondrial/genetics ; *Embryonic Development/radiation effects/genetics ; *Mitochondrial Dynamics/radiation effects ; Palaemonidae/genetics/embryology/radiation effects ; Phylogeny ; Mitochondria/metabolism/radiation effects/genetics ; Gene Expression Regulation, Developmental/radiation effects ; Embryo, Nonmammalian/radiation effects/metabolism ; },
abstract = {Studies using the embryos of the freshwater prawn Macrobrachium olfersii have reported changes in embryonic cells after exposure to ultraviolet B (UVB) radiation, such as DNA damage and apoptosis activation. Considering the importance of mitochondria in embryonic cells, this study aimed to characterize the aspects of mitochondrial morphofunctionality in M. olfersii embryos and mitochondrial responses to UVB radiation exposure. The coding sequences of genes Tfam, Nrf1, Mfn1, and Drp1 were identified from the transcriptome of M. olfersii embryos. The phylogenetic relationship showed strong amino acid identity and a highly conserved nature of the sequences. Additionally, the number of mitochondrial DNA (mtDNA) copies were higher in the early embryonic days. The results showed that the expression of the analyzed genes was highly regulated during embryonic development, increasing their levels near hatching. Furthermore, when embryos were exposed to UVB radiation, mitochondrial biogenesis was activated, recognized by higher levels of transcripts of genes Tfam and Nrf1, accompanied by mitochondrial fission. Additionally, these mitochondrial events were supported by an increase of mtDNA copies. Our results showed that UVB radiation was able to change the mitochondrial morphofunctionality, and under the current knowledge, certainly compromise embryonic cellular integrity. Additionally, mitochondria is an important cellular target of this radiation and its responses can be used to assess environmental stress caused by UVB radiation in embryos of aquatic species.},
}

Animals
*Ultraviolet Rays
*DNA, Mitochondrial/genetics
*Embryonic Development/radiation effects/genetics
*Mitochondrial Dynamics/radiation effects
Palaemonidae/genetics/embryology/radiation effects
Phylogeny
Mitochondria/metabolism/radiation effects/genetics
Gene Expression Regulation, Developmental/radiation effects
Embryo, Nonmammalian/radiation effects/metabolism

@article {pmid39759086,
year = {2024},
author = {Zou, J and Liu, Y and Tian, C and Wang, L and Li, S and Ran, J and Yang, X and Nie, G and Peng, W},
title = {Understanding the Complexity of Hypertension with Sarcopenia by Scientometric Analysis.},
journal = {Journal of multidisciplinary healthcare},
volume = {17},
number = {},
pages = {6211-6228},
pmid = {39759086},
issn = {1178-2390},
abstract = {OBJECTIVE: The scientometric analysis was aim to focus on recent studies and clarify new research directions on hypertension with sarcopenia. We hope to provide comprehensive insights or actionable recommendations for clinicians or policymakers.

METHODS: The Web of Science Core Collection database (WoSCC) from 2004 to 2023 for analysis was used. And VOSviewer, CiteSpace, and Origin software were utilized for scientometric analyses.

RESULTS: The United States was the primary contributor to 1,994 studies on hypertension with sarcopenia. The University of São Paulo emerged as the most prolific institution, with Morrell Nicholas W. being the most influential scholar and Cruz-Jentoft A.J. being the most co-cited author. PLoS One was the most prolific journal, whereas Circulation was the most relevant journal. Research has focused not only on physiological, biochemical, and cell biological mechanisms but also on sarcopenia associated with other diseases and involved in various fields, highlighting the complexity of the area and the need for integrative treatment. Keyword analysis revealed that, in addition to hypertension and sarcopenia, other topics such as obesity, pulmonary hypertension, old age, metabolic syndrome, inflammation, hypoxia, exercise, insulin resistance, and revascularization attracted attention. In recent years, COVID-19, mitochondria, handgrip strength, etc. have been hot topics, but aging, skeletal muscle, weight loss, diabetes, obesity, metabolic syndrome, insulin resistance, heart failure, mitochondria, mortality, exercise, and physical activity seems to bridge hypertension and sarcopenia research.

CONCLUSION: This study highlights the distribution of fields, the structure of knowledge and the evolution of major research topics related to hypertension in patients with sarcopenia. Identifying keyword hotspots enhanced the comprehension of occurrence, development, and future research trends related to the topic.},
}

@article {pmid39732540,
year = {2025},
author = {Golomb, R and Dahan, O and Dahary, D and Pilpel, Y},
title = {Cell-autonomous adaptation: an overlooked avenue of adaptation in human evolution.},
journal = {Trends in genetics : TIG},
volume = {41},
number = {1},
pages = {12-22},
doi = {10.1016/j.tig.2024.10.009},
pmid = {39732540},
issn = {0168-9525},
mesh = {Humans ; *Adaptation, Physiological/genetics ; *Biological Evolution ; Mitochondria/genetics/metabolism ; Selection, Genetic/genetics ; Animals ; Evolution, Molecular ; },
abstract = {Adaptation to environmental conditions occurs over diverse evolutionary timescales. In multi-cellular organisms, adaptive traits are often studied in tissues/organs relevant to the environmental challenge. We argue for the importance of an underappreciated layer of evolutionary adaptation manifesting at the cellular level. Cell-autonomous adaptations (CAAs) are inherited traits that boost organismal fitness by enhancing individual cell function. For instance, the cell-autonomous enhancement of mitochondrial oxygen utilization in hypoxic environments differs from an optimized erythropoiesis response, which involves multiple tissues. We explore the breadth of CAAs across challenges and highlight their counterparts in unicellular organisms. Applying these insights, we mine selection signals in Andean highlanders, revealing novel candidate CAAs. The conservation of CAAs across species may reveal valuable insights into multi-cellular evolution.},
}

Humans
*Adaptation, Physiological/genetics
*Biological Evolution
Mitochondria/genetics/metabolism
Selection, Genetic/genetics
Animals
Evolution, Molecular

@article {pmid39732307,
year = {2024},
author = {Wang, Z and Sun, W and Zhang, K and Ke, X and Wang, Z},
title = {New insights into the relationship of mitochondrial metabolism and atherosclerosis.},
journal = {Cellular signalling},
volume = {127},
number = {},
pages = {111580},
doi = {10.1016/j.cellsig.2024.111580},
pmid = {39732307},
issn = {1873-3913},
abstract = {Atherosclerotic cardiovascular and cerebrovascular diseases are the number one killer of human health. In view of the important role of mitochondria in the formation and evolution of atherosclerosis, our manuscript aims to comprehensively elaborate the relationship between mitochondria and the formation and evolution of atherosclerosis from the aspects of mitochondrial dynamics, mitochondria-organelle interaction (communication), mitochondria and cell death, mitochondria and vascular smooth muscle cell phenotypic switch, etc., which is combined with genome, transcriptome and proteome, in order to provide new ideas for the pathogenesis of atherosclerosis and the diagnosis and treatment of related diseases.},
}

@article {pmid39703908,
year = {2024},
author = {Li, W and Yang, Z and Yan, C and Chen, S and Zhao, X},
title = {The relationship between mitochondrial DNA haplotype and its copy number on body weight and morphological traits of Wuliangshan black-bone chickens.},
journal = {PeerJ},
volume = {12},
number = {},
pages = {e17989},
pmid = {39703908},
issn = {2167-8359},
mesh = {Animals ; *Chickens/genetics/anatomy & histology ; *Haplotypes/genetics ; *DNA, Mitochondrial/genetics ; *Body Weight/genetics ; Female ; *DNA Copy Number Variations ; Phylogeny ; Phenotype ; },
abstract = {Mitochondria play a pivotal role as carriers of genetic information through their circular DNA molecules. The rapid evolution of the D-loop region in mitochondria makes it an ideal molecular marker for exploring genetic differentiation among individuals within species and populations with close kinship. However, the influence of mtDNA D-loop region haplotypes and mtDNA copy numbers on phenotypic traits, particularly production traits in chickens, remains poorly understood. In this comprehensive study, we conducted D-loop region amplification and sequencing in the blood mitochondria of 232 female Wuliangshan black-bone chickens. Our investigation identified a total of 38 haplotypes, with a focus on 10 haplotypes that included more than five individuals. We meticulously analyzed the correlations between these haplotypes and a range of traits, encompassing body weight, tibial length, tibial circumference, body oblique length, chest width, and chest depth. The results unveiled significant disparities in specific tested traits across different haplotypes, indicating a tangible association between mtDNA haplotypes and traits in chickens. These findings underscore the potential impact of mitochondrial DNA variations on energy metabolism, ultimately leading to divergent chicken phenotypes. Furthermore, our examination revealed positive correlations between mtDNA copy numbers and tested traits for select haplotypes, while other haplotypes exhibited non-uniform relationships between traits and mtDNA copy numbers. In addition, phylogenetic analysis disclosed the involvement of two subspecies of red jungle chicken in the origin of Wuliangshan black-bone chickens. Consequently, our research contributes novel insights into mitochondrial genomic selection, augments comprehension of the roles played by haplotypes and mtDNA copy numbers in chicken population genetics and phylogenetic analysis, and furnishes fundamental data crucial for the preservation and provenance determination of black-bone chickens.},
}

Animals
*Chickens/genetics/anatomy & histology
*Haplotypes/genetics
*DNA, Mitochondrial/genetics
*Body Weight/genetics
Female
*DNA Copy Number Variations
Phylogeny
Phenotype

@article {pmid39122659,
year = {2024},
author = {Rhodes, EM and Yap, KN and Hill, GE and Hood, WR},
title = {A Comparison of the Mitochondrial Performance between Migratory and Sedentary Mimid Thrushes.},
journal = {Integrative and comparative biology},
volume = {64},
number = {6},
pages = {1859-1870},
doi = {10.1093/icb/icae137},
pmid = {39122659},
issn = {1557-7023},
support = {//Auburn University/ ; OIA1736150//National Science Foundation/ ; //Society for the Study of Evolution/ ; },
mesh = {Animals ; *Animal Migration/physiology ; Songbirds/physiology ; Flight, Animal/physiology ; Mitochondria/physiology ; Citrate (si)-Synthase/metabolism ; Species Specificity ; Pectoralis Muscles/physiology ; },
abstract = {Birds exhibit a variety of migration strategies. Because sustained flapping flight requires the production of elevated levels of energy compared to typical daily activities, migratory birds are well-documented to have several physiological adaptations to support the energy demands of migration. However, even though mitochondria are the source of ATP that powers flight, the respiratory performance of the mitochondria is almost unstudied in the context of migration. We hypothesized that migratory species would have higher mitochondrial respiratory performance during migration compared to species that do not migrate. To test this hypothesis, we compared variables related to mitochondrial respiratory function between two confamilial bird species-the migratory Gray Catbird (Dumetella carolinensis) and the non-migratory Northern Mockingbird (Mimus polyglottos). Birds were captured at the same location along the Alabama Gulf Coast, where we assumed that Gray Catbirds were migrants and where resident Northern Mockingbirds live year-round. We found a trend in citrate synthase activity, which suggests that Gray Catbirds have a greater mitochondrial volume in their pectoralis muscle, but we observed no other differences in mitochondrial respiration or complex enzymatic activities between individuals from the migrant vs. the non-migrant species. However, when we assessed the catbirds included in our study using well-established indicators of migratory physiology, birds fell into two groups: a group with physiological parameters indicating a physiology of birds engaged in migration and a group with the physiology of birds not migrating. Thus, our comparison included catbirds that appeared to be outside of migratory condition. When we compared the mitochondrial performance of these three groups, we found that the mitochondrial respiratory capacity of migrating catbirds was very similar to that of Northern Mockingbirds, while the catbirds judged to be not migrating were lowest. One explanation for these observations is these species display very different daily flight behaviors. While the mockingbirds we sampled were not breeding nor migrating, they are highly active birds, living in the open and engaging in flapping flights throughout each day. In contrast, Gray Catbirds live in shrubs and fly infrequently when not migrating. Such differences in baseline energy needs likely confounded our attempt to study adaptations to migration.},
}

Animals
*Animal Migration/physiology
Songbirds/physiology
Flight, Animal/physiology
Mitochondria/physiology
Citrate (si)-Synthase/metabolism
Species Specificity
Pectoralis Muscles/physiology

@article {pmid39701103,
year = {2024},
author = {Smith, TB and Kopajtich, R and Demain, LAM and Rea, A and Thomas, HB and Schiff, M and Beetz, C and Joss, S and Conway, GS and Shukla, A and Yeole, M and Radhakrishnan, P and Azzouz, H and Ben Chehida, A and Elmaleh-Bergès, M and Glasgow, RIC and Thompson, K and Oláhová, M and He, L and Jenkinson, EM and Jahic, A and Belyantseva, IA and Barzik, M and Urquhart, JE and O'Sullivan, J and Williams, SG and Bhaskar, SS and Carrera, S and Blakes, AJM and Banka, S and Yue, WW and Ellingford, JM and Houlden, H and , and Munro, KJ and Friedman, TB and Taylor, RW and Prokisch, H and O'Keefe, RT and Newman, WG},
title = {Bi-allelic variants in DAP3 result in reduced assembly of the mitoribosomal small subunit with altered apoptosis and a Perrault-syndrome-spectrum phenotype.},
journal = {American journal of human genetics},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajhg.2024.11.007},
pmid = {39701103},
issn = {1537-6605},
abstract = {The mitochondrial ribosome (mitoribosome) synthesizes 13 protein subunits of the oxidative phosphorylation system encoded by the mitochondrial genome. The mitoribosome is composed of 12S rRNA, 16S rRNA, and 82 mitoribosomal proteins encoded by nuclear genes. To date, variants in 12 genes encoding mitoribosomal proteins are associated with rare monogenic disorders and frequently show combined oxidative phosphorylation deficiency. Here, we describe five unrelated individuals with bi-allelic variants in death-associated protein 3 (DAP3), a nuclear gene encoding mitoribosomal small subunit 29 (MRPS29), with variable clinical presentations ranging from Perrault syndrome (sensorineural hearing loss and ovarian insufficiency) to an early childhood neurometabolic phenotype. Assessment of respiratory-chain function and proteomic profiling of fibroblasts from affected individuals demonstrated reduced MRPS29 protein amounts and, consequently, decreased levels of additional protein components of the mitoribosomal small subunit, as well as an associated combined deficiency of complexes I and IV. Lentiviral transduction of fibroblasts from affected individuals with wild-type DAP3 cDNA increased DAP3 mRNA expression and partially rescued protein levels of MRPS7, MRPS9, and complex I and IV subunits, demonstrating the pathogenicity of the DAP3 variants. Protein modeling suggested that DAP3 disease-associated missense variants can impact ADP binding, and in vitro assays demonstrated that DAP3 variants can consequently reduce both intrinsic and extrinsic apoptotic sensitivity, DAP3 thermal stability, and DAP3 GTPase activity. Our study presents genetic and functional evidence that bi-allelic variants in DAP3 result in a multisystem disorder of combined oxidative phosphorylation deficiency with pleiotropic presentations, consistent with mitochondrial dysfunction.},
}

@article {pmid39495610,
year = {2024},
author = {Tian, X and Li, F and Lin, J and Xu, Y and Tian, K and Gu, L and Zhang, Y and Xu, JR and Wang, Q},
title = {Ancient duplications, multidimensional specializations, and defense role of hexokinases in wheat.},
journal = {The Plant journal : for cell and molecular biology},
volume = {120},
number = {6},
pages = {2456-2467},
doi = {10.1111/tpj.17122},
pmid = {39495610},
issn = {1365-313X},
support = {2022YFD1400100//National Key Research and Development Program of China/ ; 32072505//National Natural Science Foundation of China/ ; 32370212//National Natural Science Foundation of China/ ; },
mesh = {*Triticum/genetics/enzymology/immunology ; *Hexokinase/genetics/metabolism ; *Plant Proteins/genetics/metabolism ; *Gene Duplication ; *Phylogeny ; Gene Expression Regulation, Plant ; Plant Diseases/genetics/immunology/microbiology ; Mitochondria/genetics/enzymology/metabolism ; },
abstract = {Hexokinases (HXKs), which sense and catalyze cellular sugar, play a critical role in the growth and development of various plants, including wheat, a primary source of human calories frequently attacked by fungal pathogens. However, the evolutionary dynamics and functional diversification of HXKs in wheat, particularly their roles in plant defense, remain unclear. Here, we discovered that the wheat hexokinase gene family originated through multiple ancient gene duplications across different plant lineages and has undergone comprehensive, multidimensional functional specialization in gene expression, subcellular localization, enzyme activity, and regulation of plant defense responses. Gene expression analysis suggests that two-thirds of the TaHXK genes are responsive to fungal infection. Subcellular analysis reveals that while six TaHXKs are localized in mitochondria, three TaHXKs from different phylogenetic branches are sorted into other cellular compartments. Notably, biochemical analysis shows that TaHXKs in mitochondria differ in their glucose-catalyzing activity, with TaHXK5 and TaHXK3 exhibiting the highest and lowest enzyme activity, respectively. Consistently, transient expression analysis suggests that TaHXK5 induces various plant defense responses, while TaHXK3 is defective in activating some plant defense responses. Furthermore, inactivation of the glucokinase activity of TaHXK5 compromised its function in defense activation, suggesting that mitochondrial TaHXKs display functional divergence in both enzyme activity and defense-inducing activity that are intrinsically connected. Overall, our findings reveal that the multidimensional specialization events following the ancient duplication events may have shaped the functional diversity of HXKs in wheat, shedding light on their evolutionary dynamics and potentially contributing to the improvement of wheat defense.},
}

*Triticum/genetics/enzymology/immunology
*Hexokinase/genetics/metabolism
*Plant Proteins/genetics/metabolism
*Gene Duplication
*Phylogeny
Gene Expression Regulation, Plant
Plant Diseases/genetics/immunology/microbiology
Mitochondria/genetics/enzymology/metabolism

@article {pmid39693336,
year = {2024},
author = {DeTar, RA and Chustecki, JM and Martinez-Hottovy, A and Ceriotti, LF and Broz, AK and Lou, X and Sanchez-Puerta, MV and Elowsky, C and Christensen, AC and Sloan, DB},
title = {Photosynthetic demands on translational machinery drive retention of redundant tRNA metabolism in plant organelles.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {52},
pages = {e2421485121},
doi = {10.1073/pnas.2421485121},
pmid = {39693336},
issn = {1091-6490},
support = {MCB-2322154//NSF (NSF)/ ; MCB-2048407//NSF (NSF)/ ; MCB-1933590//NSF (NSF)/ ; IOS-2208908//NSF (NSF)/ ; N/A//University of Nebraska Foundation/ ; },
mesh = {*Photosynthesis ; *Protein Biosynthesis ; *RNA, Transfer/metabolism/genetics ; *Amino Acyl-tRNA Synthetases/metabolism/genetics ; *Mitochondria/metabolism ; *Plastids/metabolism/genetics ; Organelles/metabolism ; Cytosol/metabolism ; Evolution, Molecular ; },
abstract = {Eukaryotic nuclear genomes often encode distinct sets of translation machinery for function in the cytosol vs. organelles (mitochondria and plastids). This raises questions about why multiple translation systems are maintained even though they are capable of comparable functions and whether they evolve differently depending on the compartment where they operate. These questions are particularly interesting in plants because translation machinery, including aminoacyl-transfer RNA (tRNA) synthetases (aaRS), is often dual-targeted to the plastids and mitochondria. These organelles have different functions, with much higher rates of translation in plastids to supply the abundant, rapid-turnover proteins required for photosynthesis. Previous studies have indicated that plant organellar aaRS evolve more slowly compared to mitochondrial aaRS in eukaryotes that lack plastids. Thus, we investigated the evolution of nuclear-encoded organellar and cytosolic aaRS and tRNA maturation enzymes across a broad sampling of angiosperms, including nonphotosynthetic (heterotrophic) plant species with reduced plastid gene expression, to test the hypothesis that translational demands associated with photosynthesis constrain the evolution of enzymes involved in organellar tRNA metabolism. Remarkably, heterotrophic plants exhibited wholesale loss of many organelle-targeted aaRS and other enzymes, even though translation still occurs in their mitochondria and plastids. These losses were often accompanied by apparent retargeting of cytosolic enzymes and tRNAs to the organelles, sometimes preserving aaRS-tRNA charging relationships but other times creating surprising mismatches between cytosolic aaRS and mitochondrial tRNA substrates. Our findings indicate that the presence of a photosynthetic plastid drives the retention of specialized systems for organellar tRNA metabolism.},
}

*Photosynthesis
*Protein Biosynthesis
*RNA, Transfer/metabolism/genetics
*Amino Acyl-tRNA Synthetases/metabolism/genetics
*Mitochondria/metabolism
*Plastids/metabolism/genetics
Organelles/metabolism
Cytosol/metabolism
Evolution, Molecular

@article {pmid39688921,
year = {2024},
author = {Alvarenga, JP and Stata, M and Sage, RF and Patel, R and das Chagas Mendonca, AM and Torre, FD and Liu, H and Cheng, S and Weake, S and Watanabe, EJ and Viana, PL and de Castro Arruda, IA and Ludwig, M and Alves Delfino Barbosa, JPR and Sage, TL},
title = {Evolutionary diversification of C2 photosynthesis in the grass genus Homolepis (Arthropogoninae).},
journal = {Annals of botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/aob/mcae214},
pmid = {39688921},
issn = {1095-8290},
abstract = {BACKGROUND AND AIMS: To better understand C4 evolution in monocots, we characterized C3-C4 intermediate phenotypes in the grass genus Homolepis (subtribe Arthropogoninae).

METHODS: Carbon isotope ratio (δ13C), leaf gas exchange, mesophyll (M) to bundle sheath (BS) tissue characteristics, organelle size and numbers in M and BS tissue, and tissue distribution of the P-subunit of glycine decarboxylase (GLDP) were determined for five Homolepis species and the C4 grass Mesosetum loliiforme from a phylogenetic sister clade. We generated a transcriptome-based phylogeny for Homolepis and Mesosetum species to interpret physiological and anatomical patterns in an evolutionary context, and to test for hybridization.

KEY RESULTS: Homolepis contains two C3 (H. glutinosa, H. villaricensis), one weaker form of C2 termed sub-C2 (H. isocalycia), and two C2 species (H. longispicula, H. aturensis). Homolepis longispicula and H. aturensis express over 85% of leaf GDC in centripetal mitochondria within the BS, and have increased fractions of leaf chloroplasts, mitochondria and peroxisomes within the BS relative to H. glutinosa. Analysis of leaf gas exchange, cell ultrastructural, and transcript expression show M. loliiforme is a C4 plant of the NADP-malic enzyme subtype. Homolepis is comprised of two sister clades, one containing H. glutinosa and H. villaricensis and the second H. longispicula and H. aturensis. Homolepis isocalycia is of hybrid origin, with parents being H. aturensis and a common ancestor of the C3  Homolepis clade and H. longispicula.

CONCLUSIONS: Photosynthetic activation of BS tissue in the sub-C2 and C2 species of Homolepis is similar to patterns observed in C3-C4 intermediate eudicots, indicating common evolutionary pathways from C3 to C4 photosynthesis in these disparate clades. Hybridization can diversify the C3-C4 intermediate character state and should be considered in reconstructing putative ancestral states using phylogenetic analyses.},
}

@article {pmid39688736,
year = {2024},
author = {Singha, D and Patidar, A and Pal, S and Tyagi, K and Kumar, V},
title = {Mitochondrial genetic diversity of pest and vector species, Frankliniella schultzei (Thripidae: Thripinae).},
journal = {Molecular biology reports},
volume = {52},
number = {1},
pages = {55},
pmid = {39688736},
issn = {1573-4978},
support = {CRG/2023/000498//Science and Engineering Research Board/ ; },
mesh = {Animals ; *Phylogeny ; *Genetic Variation/genetics ; *Haplotypes/genetics ; India ; *Thysanoptera/genetics/classification ; DNA Barcoding, Taxonomic/methods ; Australia ; DNA, Mitochondrial/genetics ; Mitochondria/genetics ; Insect Vectors/genetics/classification ; Bayes Theorem ; Gene Flow ; },
abstract = {BACKGROUND: Frankliniella schultzei (Trybom) is a serious pest and a carrier of tospoviruses in major agricultural crops. This species is a historical and unresolved species complex that contains genetically different cryptic species across the globe.

METHODS AND RESULTS: DNA barcodes were generated from freshly collected specimens of F. schultzei from India and Australia using the sanger sequencing. Seventy-five COI sequences were generated from India and Australia. Moreover, 318 sequences were downloaded (India, Australia, Pakistan, and Africa) from the NCBI GenBank to explore the genetic diversity and phylogeny. The minimum and maximum mean interspecific distance between 393 sequences was found to be 7.97% and 21.50%, respectively. Bayesian and Neighbour joining clustering indicated the presence of five putative species within F. schultzei that had sympatry and allopatry. Moreover, 20 haplotypes and 140 polymorphic sites were identified. The African clade is unique; it does not share haplotypes with any other countries, suggesting it may represent the true F. schultzei. Haplotype network analysis showed shallow gene flow and deep genetic variation between the populations. Signatures of recent population history events were measured using Fu's Fs test and Tajima's D test. Morphometric analysis based on seven characters is also carried out.

CONCLUSION: Phylogeny and genetic distance revealed the presence of five putative species within F. schultzei. On the contrary, morphology does not unequivocally corroborate the phylogenetic results, as morphometric analysis showed overlap among these clades. To resolve F. schultzei species complex, whole genome-based sequencing data are very much necessitated.},
}

Animals
*Phylogeny
*Genetic Variation/genetics
*Haplotypes/genetics
India
*Thysanoptera/genetics/classification
DNA Barcoding, Taxonomic/methods
Australia
DNA, Mitochondrial/genetics
Mitochondria/genetics
Insect Vectors/genetics/classification
Bayes Theorem
Gene Flow

@article {pmid39677574,
year = {2024},
author = {Bettinazzi, S and Liang, J and Rodriguez, E and Bonneau, M and Holt, R and Whitehead, B and Dowling, DK and Lane, N and Camus, MF},
title = {Assessing the role of mitonuclear interactions on mitochondrial function and organismal fitness in natural Drosophila populations.},
journal = {Evolution letters},
volume = {8},
number = {6},
pages = {916-926},
pmid = {39677574},
issn = {2056-3744},
abstract = {Mitochondrial function depends on the effective interactions between proteins and RNA encoded by the mitochondrial and nuclear genomes. Evidence suggests that both genomes respond to thermal selection and promote adaptation. However, the contribution of their epistatic interactions to life history phenotypes in the wild remains elusive. We investigated the evolutionary implications of mitonuclear interactions in a real-world scenario that sees populations adapted to different environments, altering their geographical distribution while experiencing flow and admixture. We created a Drosophila melanogaster panel with replicate native populations from the ends of the Australian east-coast cline, into which we substituted the mtDNA haplotypes that were either predominant or rare at each cline-end, thus creating putatively mitonuclear matched and mismatched populations. Our results suggest that mismatching may impact phenotype, with populations harboring the rarer mtDNA haplotype suffering a trade-off between aerobic capacity and key fitness aspects such as reproduction, growth, and survival. We discuss the significance of mitonuclear interactions as modulators of life history phenotypes in the context of future adaptation and population persistence.},
}

@article {pmid39676593,
year = {2024},
author = {Coronel, FP and Gras, DE and Canal, MV and Roldan, F and Welchen, E and Gonzalez, DH},
title = {Cytochrome c levels link mitochondrial function to plant growth and stress responses through changes in SnRK1 pathway activity.},
journal = {The Plant journal : for cell and molecular biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/tpj.17215},
pmid = {39676593},
issn = {1365-313X},
support = {PICT-2020-0362//Fondo para la Investigación Científica y Tecnológica/ ; PICT-2021-00486//Fondo para la Investigación Científica y Tecnológica/ ; CAI+D-2020//Universidad Nacional del Litoral/ ; },
abstract = {Energy is required for growth as well as for multiple cellular processes. During evolution, plants developed regulatory mechanisms to adapt energy consumption to metabolic reserves and cellular needs. Reduced growth is often observed under stress, leading to a growth-stress trade-off that governs plant performance under different conditions. In this work, we report that plants with reduced levels of the mitochondrial respiratory chain component cytochrome c (CYTc), required for electron transport coupled to oxidative phosphorylation and ATP production, show impaired growth and increased global expression of stress-responsive genes, similar to those observed after inhibiting the respiratory chain or the mitochondrial ATP synthase. CYTc-deficient plants also show activation of the SnRK1 pathway, which regulates growth, metabolism, and stress responses under carbon starvation conditions, even though their carbohydrate levels are not significantly different from wild-type. Notably, loss-of-function of the gene encoding the SnRK1α1 subunit restores the growth of CYTc-deficient plants, as well as autophagy, free amino acid and TOR pathway activity levels, which are affected in these plants. Moreover, increasing CYTc levels decreases SnRK1 pathway activation, reflected in reduced SnRK1α1 phosphorylation, with no changes in total SnRK1α1 protein levels. Under stress imposed by mannitol, the growth of CYTc-deficient plants is relatively less affected than that of wild-type plants, which is also related to the activation of the SnRK1 pathway. Our results indicate that SnRK1 function is affected by CYTc levels, thus providing a molecular link between mitochondrial function and plant growth under normal and stress conditions.},
}

@article {pmid39665281,
year = {2024},
author = {Crino, OL and Wild, KH and Friesen, CR and Leibold, D and Laven, N and Peardon, AY and Recio, P and Salin, K and Noble, DWA},
title = {From eggs to adulthood: sustained effects of early developmental temperature and corticosterone exposure on physiology and body size in an Australian lizard.},
journal = {The Journal of experimental biology},
volume = {227},
number = {24},
pages = {},
doi = {10.1242/jeb.249234},
pmid = {39665281},
issn = {1477-9145},
support = {DP210101152//Australian Research Council/ ; //Australian National University/ ; },
mesh = {Animals ; *Corticosterone/pharmacology ; *Lizards/physiology/growth & development ; *Body Size/drug effects ; *Temperature ; Female ; Ovum/drug effects/physiology ; Australia ; Male ; },
abstract = {Developing animals are increasingly exposed to elevated temperatures as global temperatures rise as a result of climate change. Vertebrates can be affected by elevated temperatures during development directly, and indirectly through maternal effects (e.g. exposure to prenatal glucocorticoid hormones). Past studies have examined how elevated temperatures and glucocorticoid exposure during development independently affect vertebrates. However, exposure to elevated temperatures and prenatal corticosterone could have interactive effects on developing animals that affect physiology and life-history traits across life. We tested interactions between incubation temperature and prenatal corticosterone exposure in the delicate skink (Lampropholis delicata). We treated eggs with high or low doses of corticosterone and incubated eggs at 23°C (cool) or 28°C (warm). We measured the effects of these treatments on development time, body size and survival from hatching to adulthood and on adult hormone levels and mitochondrial respiration. We found no evidence for interactive effects of incubation temperature and prenatal corticosterone exposure on phenotype. However, incubation temperature and corticosterone treatment each independently decreased body size at hatching and these effects were sustained into the juvenile period and adulthood. Lizards exposed to low doses of corticosterone during development had elevated levels of baseline corticosterone as adults. Additionally, lizards incubated at cool temperatures had higher levels of baseline corticosterone and more efficient mitochondria as adults compared with lizards incubated at warm temperatures. Our results show that developmental conditions can have sustained effects on morphological and physiological traits in oviparous lizards but suggest that incubation temperature and prenatal corticosterone do not have interactive effects.},
}

Animals
*Corticosterone/pharmacology
*Lizards/physiology/growth & development
*Body Size/drug effects
*Temperature
Female
Ovum/drug effects/physiology
Australia
Male

@article {pmid39661651,
year = {2024},
author = {Prediger, C and Ferreira, EA and Videira Zorzato, S and Hua-Van, A and Klasson, L and Miller, WJ and Yassin, A and Madi-Ravazzi, L},
title = {Saltational episodes of reticulate evolution in the Drosophila saltans species group.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msae250},
pmid = {39661651},
issn = {1537-1719},
abstract = {Phylogenomics reveals reticulate evolution to be widespread across taxa, but whether reticulation is due to low statistical power or it is a true evolutionary pattern remains a field of study. Here, we investigate the phylogeny and quantify reticulation in the Drosophila saltans species group, a Neotropical clade of the subgenus Sophophora comprising 23 species whose relationships have long been problematic. Phylogenetic analyses revealed conflicting topologies between the X chromosome, autosomes and the mitochondria. We extended the ABBA-BABA test of asymmetry in phylogenetic discordance to cases where no "true" species tree could be inferred, and applied our new test (called 2A2B) to whole genome data and to individual loci. We used four strategies, two based on our new assemblies using either conserved genes or ≥50 kb-long syntenic blocks with conserved collinearity across Neotropical Sophophora, and two consisted of windows from pseudo-reference genomes aligned to either an ingroup or outgroup species. Evidence for reticulation varied among the strategies, being lowest in the synteny-based approach, where it did not exceed ∼7% of the blocks in the most conflicting species quartets. High incidences of reticulation were restricted to three nodes on the tree, that coincided with major paleogeographical events in South America. Our results identify possible technical biases in quantifying reticulate evolution and indicate that episodic rapid radiations have played a major role in the evolution of a largely understudied Neotropical clade.},
}

@article {pmid39658314,
year = {2024},
author = {Sørensen, MES and Stiller, ML and Kröninger, L and Nowack, ECM},
title = {Protein import into bacterial endosymbionts and evolving organelles.},
journal = {The FEBS journal},
volume = {},
number = {},
pages = {},
doi = {10.1111/febs.17356},
pmid = {39658314},
issn = {1742-4658},
support = {101061817//H2020 European Research Council/ ; //Deutsche Forschungsgemeinschaft/ ; },
abstract = {Bacterial endosymbionts are common throughout the eukaryotic tree of life and provide a range of essential functions. The intricate integration of bacterial endosymbionts into a host led to the formation of the energy-converting organelles, mitochondria and plastids, that have shaped eukaryotic evolution. Protein import from the host has been regarded as one of the distinguishing features of organelles as compared to endosymbionts. In recent years, research has delved deeper into a diverse range of endosymbioses and discovered evidence for 'exceptional' instances of protein import outside of the canonical organelles. Here we review the current evidence for protein import into bacterial endosymbionts. We cover both 'recently evolved' organelles, where there is evidence for hundreds of imported proteins, and endosymbiotic systems where currently only single protein import candidates are described. We discuss the challenges of establishing protein import machineries and the diversity of mechanisms that have independently evolved to solve them. Understanding these systems and the different independent mechanisms, they have evolved is critical to elucidate how cellular integration arises and deepens at the endosymbiont to organelle interface. We finish by suggesting approaches that could be used in the future to address the open questions. Overall, we believe that the evidence now suggests that protein import into bacterial endosymbionts is more common than generally realized, and thus that there is an increasing number of partnerships that blur the distinction between endosymbiont and organelle.},
}

@article {pmid39536732,
year = {2024},
author = {Xuan, D and Qiang, F and Xu, H and Wang, L and Xia, Y},
title = {Screening for Mitochondrial tRNA Variants in 200 Patients with Systemic Lupus Erythematosus.},
journal = {Human heredity},
volume = {89},
number = {1},
pages = {84-97},
doi = {10.1159/000542357},
pmid = {39536732},
issn = {1423-0062},
mesh = {Humans ; *Lupus Erythematosus, Systemic/genetics ; *RNA, Transfer/genetics ; Female ; Male ; Adult ; DNA, Mitochondrial/genetics ; Middle Aged ; RNA, Mitochondrial/genetics ; Reactive Oxygen Species/metabolism ; Mitochondria/genetics ; Mutation/genetics ; Case-Control Studies ; Phylogeny ; Membrane Potential, Mitochondrial/genetics ; Genetic Predisposition to Disease ; },
abstract = {INTRODUCTION: Systemic lupus erythematosus (SLE) is a common autoimmune disease with unknown etiology. Recently, a growing number of evidence suggested that mitochondrial dysfunctions played active roles in the pathogenesis of SLE, but its detailed mechanism remains largely undetermined. The aim of this study was to analyze the frequencies of mitochondrial tRNA (mt-tRNA) variants in Chinese individuals with SLE.

METHODS: We carried out a mutational screening of mt-tRNA variants in a cohort of 200 patients with SLE and 200 control subjects by PCR-Sanger sequencing. The potential pathogenicity of mt-tRNA variants was evaluated by phylogenetic conservation and haplogroup analyses. In addition, trans-mitochondrial cybrid cell lines were established, and mitochondrial functions including ATP, reactive oxygen species (ROS), mitochondrial DNA (mtDNA) copy number, mitochondrial membrane potential (MMP), superoxide dismutase (SOD), and mt-RNA transcription were analyzed in cybrids with and without these putative pathogenic mt-tRNA variants.

RESULTS: We identified five possible pathogenic variants: tRNAVal G1606A, tRNALeu(UUR) A3243G, tRNAIle A4295G, tRNAGly T9997C, and tRNAThr A15924G that only found in SLE patients but were absent in controls. Interestingly, these variants were located at extremely conserved nucleotides of the corresponding tRNAs and may alter tRNAs' structure and function. Furthermore, cells carrying these tRNA variants had much lower levels of ATP, mtDNA copy number, MMP, and SOD than controls; by contrast, the levels of ROS increased significantly (p < 0.05 for all). Furthermore, a significant reduction in mt-ND1, ND2, ND3, ND5, and A6 mRNA expression was observed in cells with these mt-tRNA variants, while compared with controls. Thus, failures in tRNA metabolism caused by these variants would impair mitochondrial translation and subsequently lead to mitochondrial dysfunction that was involved in the progression and pathogenesis of SLE.

CONCLUSIONS: Our study suggested that mt-tRNA variants were important causes for SLE, and screening for mt-tRNA pathogenic variants was recommended for early detection and prevention for this disorder.},
}

Humans
*Lupus Erythematosus, Systemic/genetics
*RNA, Transfer/genetics
Female
Male
Adult
DNA, Mitochondrial/genetics
Middle Aged
RNA, Mitochondrial/genetics
Reactive Oxygen Species/metabolism
Mitochondria/genetics
Mutation/genetics
Case-Control Studies
Phylogeny
Membrane Potential, Mitochondrial/genetics
Genetic Predisposition to Disease

@article {pmid39648544,
year = {2024},
author = {Acharya, TK and Mahapatra, P and Kumar, S and Dubey, NK and Rajalaxmi, S and Ghosh, A and Kumar, A and Goswami, C},
title = {Conserved and Unique Mitochondrial Target Sequence of TRPV4 Can Independently Regulate Mitochondrial Functions.},
journal = {Proteins},
volume = {},
number = {},
pages = {},
doi = {10.1002/prot.26772},
pmid = {39648544},
issn = {1097-0134},
support = {BT/PR8004/MED/30/988/2013//Department of Biotechnology (DBT), Ministry of science and Technology/ ; //National Institute of Science Education and Research/ ; },
abstract = {Though mitochondria have their own genome and protein synthesis machineries, the majority of the mitochondrial proteins are actually encoded by the nuclear genome. Most of these mitochondrial proteins are imported into specific compartments of the mitochondria due to their mitochondrial target sequence (MTS). Unlike the nuclear target sequence, the MTS of most of the mitochondrial localized proteins remain poorly understood, mainly due to their variability, heterogeneity, unconventional modes of action, mitochondrial potential-dependent transport, and other complexities. Recently, we reported that transient receptor potential vanilloid subtype 4 (TRPV4), a thermosensitive cation channel, is physically located at the mitochondria. Here we characterize a small segment (AA 592-630) located at the TM4-loop4-TM5 segment of TRPV4 that acts as a novel MTS. The same region remains highly conserved in all vertebrates and contains a large number of point mutations each of which causes an diverse spectrum of diseases in human. Using confocal and super-resolution microscopy, we show that this MTS of TRPV4 or its mutants localizes to the mitochondria independently and also induces functional and quantitative changes in the mitochondria. By using conformal microscopy, we could detect the presence of the MTS region within the isolated mitochondria. These findings may be important to understand the complexity of MTS and TRPV4-induced channelopathies better.},
}

@article {pmid39633470,
year = {2024},
author = {Atherton, W and Ambrose, L and Wisdom, J and Lessard, BD and Kurucz, N and Webb, CE and Beebe, NW},
title = {Nuclear and mitochondrial population genetics of the Australasian arbovirus vector Culex annulirostris (Skuse) reveals strong geographic structure and cryptic species.},
journal = {Parasites & vectors},
volume = {17},
number = {1},
pages = {501},
pmid = {39633470},
issn = {1756-3305},
support = {RG 18-19//Australian Biological Resources Study, Australia's Department of Climate Change, Energy, the Environment and Water/ ; },
mesh = {Animals ; *Culex/genetics/classification/virology ; *Microsatellite Repeats/genetics ; *Mosquito Vectors/genetics/classification/virology ; *Genetic Variation ; Australia ; *DNA, Mitochondrial/genetics ; Genetics, Population ; Arboviruses/genetics ; Australasia/epidemiology ; Papua New Guinea ; Electron Transport Complex IV/genetics ; Haplotypes ; Phylogeny ; Mitochondria/genetics ; },
abstract = {BACKGROUND: The mosquito Culex annulirostris Skuse (Diptera: Culicidae) is an important arbovirus vector in Australasia. It is part of the Culex sitiens subgroup that also includes Cx. palpalis and Cx. sitiens. Single locus mitochondrial and nuclear DNA sequencing studies suggest that Cx. annulirostris consists of a complex of at least two species. We tested this hypothesis by analysing both nuclear microsatellite data and additional mitochondrial sequence data to describe the population genetics of Cx. annulirostris through Australia, Papua New Guinea (PNG) and the Solomon Archipelago.

METHODS: Twelve novel microsatellite markers for Cx. annulirostris were developed and used on over 500 individuals identified as Cx. annulirostris by molecular diagnostics. Ten of the 12 microsatellites then used for analysis using Discriminant Analysis of Principal Components, a Bayesian clustering software, STRUCTURE, along with estimates of Jost's D statistic that is similar to FST but better suited to microsatellite data. Mitochondrial cytochrome oxidase I (COI) DNA sequence were also generated complementing previous work and analysed for sequence diversity (Haplotype diversity, Hd and Pi, π), Tadjima's D, and pairwise FST between populations. An allele specific molecular diagnostic with an internal control was developed.

RESULTS: We confirm the existence of multiple genetically and geographically restricted populations. Within mainland Australia, our findings show that Cx. annulirostris consists of two genetically and geographically distinct populations. One population extends through northern Australia and into the south-east coast of Queensland and New South Wales (NSW). The second Australian population occurs through inland NSW, Victoria, South Australia, extending west to southern Western Australia. These two Australian populations show evidence of possible admixture in central Australia and far north Queensland. Australia's Great Dividing Range that runs down southeast Australia presents a strong gene-flow barrier between these two populations which may be driven by climate, elevation or river basins. In PNG we find evidence of reproductive isolation between sympatric cryptic species occurring through PNG and Australia's northern Cape York Peninsula. A PCR-based molecular diagnostic was developed to distinguish these two cryptic species.

CONCLUSION: This study adds to the growing body of work suggesting that the taxon presently known as Cx. annulirostris now appears to consist of at least two cryptic species that co-occur in northern Australia and New Guinea and can be distinguished by a ITS1 PCR diagnostic. The Solomon Islands population may also represent a distinct species but in light its geographic isolation and lack of sympatry with other species would require further study. Additionally, the mitochondrial and nuclear DNA evidence of population structure between geographic regions within Australia appears latitudinal and elevational driven and may suggest an additional subspecies in that hybridise where they overlap.},
}

Animals
*Culex/genetics/classification/virology
*Microsatellite Repeats/genetics
*Mosquito Vectors/genetics/classification/virology
*Genetic Variation
Australia
*DNA, Mitochondrial/genetics
Genetics, Population
Arboviruses/genetics
Australasia/epidemiology
Papua New Guinea
Electron Transport Complex IV/genetics
Haplotypes
Phylogeny
Mitochondria/genetics

@article {pmid39629328,
year = {2024},
author = {Qi, X and Wang, Z and Lin, Y and Guo, Y and Dai, Z and Wang, Q},
title = {Elucidation and engineering mitochondrial respiratory-related genes for improving bioethanol production at high temperature in Saccharomyces cerevisiae.},
journal = {Engineering microbiology},
volume = {4},
number = {2},
pages = {100108},
pmid = {39629328},
issn = {2667-3703},
abstract = {Industrial manufacturing of bioproducts, especially bioethanol, can benefit from high-temperature fermentation, which requires the use of thermotolerant yeast strains. Mitochondrial activity in yeast is closely related to its overall metabolism. However, the mitochondrial respiratory changes in response to adaptive thermotolerance are still poorly understood and have been rarely utilized for developing thermotolerant yeast cell factories. Here, adaptive evolution and transcriptional sequencing, as well as whole-genome-level gene knockout, were used to obtain a thermotolerant strain of Saccharomyces cerevisiae. Furthermore, thermotolerance and bioethanol production efficiency of the engineered strain were examined. Physiological evaluation showed the boosted fermentation capacity and suppressed mitochondrial respiratory activity in the thermotolerant strain. The improved fermentation produced an increased supply of adenosine triphosphate required for more active energy-consuming pathways. Transcriptome analysis revealed significant changes in the expression of the genes involved in the mitochondrial respiratory chain. Evaluation of mitochondria-associated gene knockout confirmed that ADK1, DOC1, or MET7 were the key factors for the adaptive evolution of thermotolerance in the engineered yeast strain. Intriguingly, overexpression of DOC1 with TEF1 promoter regulation led to a 10.1% increase in ethanol production at 42 °C. The relationships between thermotolerance, mitochondrial activity, and respiration were explored, and a thermotolerant yeast strain was developed by altering the expression of mitochondrial respiration-related genes. This study provides a better understanding on the physiological mechanism of adaptive evolution of thermotolerance in yeast.},
}

@article {pmid39623987,
year = {2024},
author = {Zhang, Y and Zang, C and Pan, X and Gong, M and Liu, H},
title = {[Population genetic diversity of Culex tritaeniorhynchus in Jining City of Shandong Province based on the mitochondrial cytochrome C oxidase I gene].},
journal = {Zhongguo xue xi chong bing fang zhi za zhi = Chinese journal of schistosomiasis control},
volume = {36},
number = {5},
pages = {466-473},
doi = {10.16250/j.32.1915.2024119},
pmid = {39623987},
issn = {1005-6661},
support = {tsqn202312373//Shandong Provincial Taishan Scholar Program/ ; ZR2R2020KH001//Key Project of Natural Science Foundation t of Shandong Province/ ; 230726153807227//University-Industry Collaborative Education Program of Ministry of Education/ ; },
mesh = {Animals ; *Culex/genetics ; *Electron Transport Complex IV/genetics ; *Genetic Variation ; China ; Haplotypes ; Phylogeny ; Female ; Mitochondria/genetics ; },
abstract = {OBJECTIVE: To understand the genetic basis of the adaptation of Culex tritaeniorhynchus to different environmental ecology in Jining City, Shandong Province, so as to provide insights into understanding of the population structure or isolation pattern of Cx. tritaeniorhynchus in the city.

METHODS: Seven sampling sites were selected from urban, suburban and rural areas of Jining City, Shandong Province from June to August 2023, and mosquitoes were collected using mosquito-trapping lamps. All collected adult mosquitoes were identified morphologically. Genomic DNA was extracted from a single female Cx. tritaeniorhynchus mosquito, and the mitochondrial cytochrome C oxidase I (COI) gene was amplified using a PCR assay, sequenced and subjected to molecular identification. The number of haplotypes, haplotype diversity (Hd), nucleotide diversity (Pi), and average number of nucleotide differences (K) of Cx. tritaeniorhynchus DNA sequences were estimated among different sampling sites using the software DnaSP 6, and a neutrality test was performed. The fixation index (FST), and gene flow (number of migrants, Nm) of Cx. tritaeniorhynchus populations were calculated using the software Arlequin 3.5.2, and subjected to analysis of molecular variance (AMOVA). In addition, a haplotype network diagrams and a phylogenetic tree of Cx. tritaeniorhynchus populations were created using the software PopART and MEGA 11, respectively.

RESULTS: A total of 420 sequences were successfully amplified from the COI gene of Cx. tritaeniorhynchus samples collected from 7 sampling sites in Jining City, and a gene fragment sequence with a length of 603 bp was obtained, with 55 variable sites and 46 haplotypes and without insertion or deletion mutations. Of the 46 haplotypes, H01 was the dominant shared haplotype, and the haplotype frequency increased gradually from urban areas (34.00%) to rural areas (47.00%). The mean Hd, Pi and K values of Cx. tritaeniorhynchus COI genes were 0.814, 0.024 and 14.129, 0.489, 0.016 and 7.941 and 0.641, 0.016 and 10.393 in suburban, urban, and rural areas, respectively, with the highest population diversity of Cx. tritaeniorhynchus in suburban areas and the lowest in urban areas. Paired FST analysis among different types of sampling sites showed that the mean FST value was 0.029 between urban and suburban areas, indicating more frequent inter-population communication. AMOVA revealed that the percentage of intra-population variation (95.74%) was higher than that of inter-population variation (4.26%). Neutrality tests showed deviation from neutrality in Cx. tritaeniorhynchus populations collected from Nanyang Township (Tajima's D = 2.793, Fu's Fs = 6.429, both P values < 0.05). In addition, the mismatch distribution curves of Cx. tritaeniorhynchus COI gene appeared bimodal or multimodal patterns in Jining City, indicating a relatively stable overall population size.

CONCLUSIONS: The mitochondrial COI gene may be used as a molecular marker to investigate the population genetic diversity of Cx. tritaeniorhynchus. The population genetic diversity of Cx. tritaeniorhynchus is higher in the suburban areas of Jining City than in rural and urban areas, and there are frequent genetic exchanges between Cx. tritaeniorhynchus populations from urban and suburban areas.},
}

Animals
*Culex/genetics
*Electron Transport Complex IV/genetics
*Genetic Variation
China
Haplotypes
Phylogeny
Female
Mitochondria/genetics

@article {pmid39623304,
year = {2024},
author = {Zhang, C and Rasool, A and Qi, H and Zou, X and Wang, Y and Wang, Y and Wang, Y and Liu, Y and Yu, Y},
title = {Comprehensive analysis of the first complete mitogenome and plastome of a traditional Chinese medicine Viola diffusa.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {1162},
pmid = {39623304},
issn = {1471-2164},
mesh = {*Genome, Mitochondrial ; *Medicine, Chinese Traditional ; *Viola/genetics ; Phylogeny ; Base Composition ; RNA, Transfer/genetics ; Genome, Plastid ; Codon Usage ; },
abstract = {BACKGROUND: Viola diffusa is used in the formulation of various Traditional Chinese Medicines (TCMs), including antiviral, antimicrobial, antitussive, and anti-inflammatory drugs, due to its richness in flavonoids and triterpenoids. The biosynthesis of these compounds is largely mediated by cytochrome P450 enzymes, which are primarily located in the membranes of mitochondria and the endoplasmic reticulum.

RESULTS: This study presents the complete assembly of the mitogenome and plastome of Viola diffusa. The circular mitogenome spans 474,721 bp with a GC content of 44.17% and encodes 36 unique protein-coding genes, 21 tRNA, and 3 rRNA. Except for the RSCU values of 1 observed for the start codon (AUG) and tryptophan (UGG), the mitochondrial protein-coding genes exhibited a codon usage bias, with most estimates deviating from 1, similar to patterns observed in closely related species. Analysis of repetitive sequences in the mitogenome demonstrated potential homologous recombination mediated by these repeats. Sequence transfer analysis revealed 24 homologous sequences shared between the mitogenome and plastome, including nine full-length genes. Collinearity was observed among Viola diffusa species within the other members of Malpighiales order, indicated by the presence of homologous fragments. The length and arrangement of collinear blocks varied, and the mitogenome exhibited a high frequency of gene rearrangement.

CONCLUSIONS: We present the first complete assembly of the mitogenome and plastome of Viola diffusa, highlighting its implications for pharmacological, evolutionary, and taxonomic studies. Our research underscores the multifaceted importance of comprehensive mitogenome analysis.},
}

*Genome, Mitochondrial
*Medicine, Chinese Traditional
*Viola/genetics
Phylogeny
Base Composition
RNA, Transfer/genetics
Genome, Plastid
Codon Usage

@article {pmid39515725,
year = {2024},
author = {Zhou, J and Wang, P and Wang, Y and Zhang, J and He, X and Wang, L},
title = {Genome-wide identification and expression analysis of SpUGE gene family and heterologous expression-mediated Arabidopsis thaliana tolerance to Cd stress.},
journal = {International journal of biological macromolecules},
volume = {282},
number = {Pt 5},
pages = {137358},
doi = {10.1016/j.ijbiomac.2024.137358},
pmid = {39515725},
issn = {1879-0003},
mesh = {*Arabidopsis/genetics ; *Cadmium/toxicity ; *Gene Expression Regulation, Plant ; *Stress, Physiological/genetics ; *Cell Wall/metabolism/genetics ; *Plants, Genetically Modified/genetics ; Multigene Family ; Plant Proteins/genetics/metabolism ; Salix/genetics/metabolism ; Genome, Plant ; Phylogeny ; Polysaccharides/metabolism ; Gene Expression Profiling ; },
abstract = {The UDP-glucose 4-epimerase (UGE) enzyme plays a critical role in plant growth and responses to abiotic stressors, such as heavy metal exposure. However, UGE-mediated remodeling of cell wall polysaccharides in response to these stressors remains poorly understood in willow. This study investigated the structure, function, and expression patterns of the UGE gene family in willow, focusing on cadmium treatment to elucidate how SpUGE1 enhances Cd resistance. Six SpUGE genes were identified through whole-genome sequencing and bioinformatics analysis, and they were mapped across five chromosomes. Quantitative PCR analysis revealed that, with the exception of SpUGE3, all genes showed their highest relative expression in the leaves. Under Cd treatment, members of the SpUGE gene family displayed varying levels of responsiveness, with SpUGE1 showing a marked increase in expression over time. In transgenic Arabidopsis thaliana overexpressing SpUGE1, the cellulose, hemicellulose, lignin, and pectin content significantly increased, with cellulose levels rising by >50 % and pectin by approximately 30 %. This overexpression conferred enhanced Cd resistance by increasing cell wall thickness through elevated cell wall polysaccharides, which reduced Cd uptake. Consequently, Cd content in the cell wall, chloroplasts, and mitochondria was significantly lower than that in wild-type plants, reducing cellular damage and improving Cd resistance. Overall, this study provides valuable theoretical and experimental insights into the role of the SpUGE1 gene family in willow.},
}

*Arabidopsis/genetics
*Cadmium/toxicity
*Gene Expression Regulation, Plant
*Stress, Physiological/genetics
*Cell Wall/metabolism/genetics
*Plants, Genetically Modified/genetics
Multigene Family
Plant Proteins/genetics/metabolism
Salix/genetics/metabolism
Genome, Plant
Phylogeny
Polysaccharides/metabolism
Gene Expression Profiling

@article {pmid39617091,
year = {2024},
author = {Zhao, J and Liang, ZL and Fang, SL and Li, RJ and Huang, CJ and Zhang, LB and Robison, T and Zhu, ZM and Cai, WJ and Yu, H and He, ZR and Zhou, XM},
title = {Phylogenomics of Paragymnopteris (Cheilanthoideae, Pteridaceae): Insights from plastome, mitochondrial, and nuclear datasets.},
journal = {Molecular phylogenetics and evolution},
volume = {},
number = {},
pages = {108253},
doi = {10.1016/j.ympev.2024.108253},
pmid = {39617091},
issn = {1095-9513},
abstract = {Previous studies have shown that at least six genera of the Cheilanthoideae, a subfamily of the fern family Pteridaceae, may not be monophyletic. In these non-monophyletic genera, the Old-World genus Paragymnopteris including approximately five species have long been controversial. In this study, with an extensive taxon sampling of Paragymnopteris, we assembled 19 complete plastomes of all recognized Paragymnopteris species, plastomes of Pellaea (3 species) and Argyrochosma (1 species), as well as transcriptomes from Paragymnopteris (6 species) and Argyrochosma (1 species). We conducted a comprehensive and systematic phylogenomic analysis focusing on the contentious relationships among the genus of Paragymnopteris through 9 plastid makers, the plastomes, mitochondria, nuclear ribosomal cistron genomes, and single-copy nuclear genes. Moreover, we further combined distribution, ploidy, and morphological features to investigate the evolution of Paragymnopteris. The backbone of Paragymnopteris was resolved consistently in the nuclear and plastid phylogenies. Our major results include: (1) Paragymnopteris is not monophyletic including two fully supported clades; (2) confirming that Paragymnopteris delavayi var. intermedia is a close relative of P. delavayi instead of P. marantae var. marantae; (3) the chromosome base number may not be a stable trait which has previously been used as an important character to divide Paragymnopteris into two groups; and (4) gene flow or introgression might be the main reason for the gene trees conflict of Paragymnopteris, but both gene flow and ILS might simultaneously and/or cumulatively act on the conflict of core pellaeids. The robust phylogeny of Paragymnopteris presented here will help us for the future studies of the arid to semi-arid ferns of Cheilanthoideae at the evolutionary, physiological, developmental, and omics-based levels.},
}

@article {pmid39547447,
year = {2025},
author = {Xin, C and Wang, J and Chi, J and Xu, Y and Liang, R and Jian, L and Wang, L and Guo, J},
title = {Intragenic cytosine methylation modification regulates the response of SUCLα1 to lower temperature in Solanaceae.},
journal = {Plant science : an international journal of experimental plant biology},
volume = {350},
number = {},
pages = {112320},
doi = {10.1016/j.plantsci.2024.112320},
pmid = {39547447},
issn = {1873-2259},
mesh = {*Cytosine/metabolism ; *Cold Temperature ; Plant Proteins/genetics/metabolism ; DNA Methylation ; Solanum tuberosum/genetics/metabolism ; Phylogeny ; Gene Expression Regulation, Plant ; Solanaceae/genetics/metabolism/physiology ; Nicotiana/genetics ; },
abstract = {The tricarboxylic acid cycle (TCAC) is a fundamental metabolic process governing matter and energy in plant cells, playing an indispensable role. However, its involvement in responding to low temperature stress in potato remains poorly understood. Previous studies have identified succinyl-CoA ligase (SUCL), which catalyzes the phosphorylation of TCAC substrates, as a gene associated with lower temperatures. Nevertheless, its function in potato's response to lower temperatures remains unclear. Phylogenetic analysis has revealed that Solanum tuberosum possesses α and β subunits of SUCL, which cluster with those of Solanum lycopersicum, Nicotiana tabacum and Nicotiana benthamiana. Further investigation has shown that StSUCLα1 is predominantly located within mitochondria. Low temperatures induce methylation modification alterations at 11 intragenic cytosine sites and lead to changes in StSUCLα1 expression levels. Correlation analysis suggests that alterations in intragenic cytosine methylation sites of SUCLα1 may be associated with MET1. Knocking down NbSUCLα1, the homologous gene of StSUCLα1 in N. benthamiana, results in increased susceptibility to low temperature stress in plants. In summary, we have confirmed that SUCLα1 is a key gene modulated by intragenic cytosine methylation in response to lower temperatures, providing a novel target for genetic breeding aimed at enhancing potato tolerance to low temperature stress.},
}

*Cytosine/metabolism
*Cold Temperature
Plant Proteins/genetics/metabolism
DNA Methylation
Solanum tuberosum/genetics/metabolism
Phylogeny
Gene Expression Regulation, Plant
Solanaceae/genetics/metabolism/physiology
Nicotiana/genetics

@article {pmid39226612,
year = {2024},
author = {Forbes, K and Barrera, M and Nielsen-Roine, K and Hersh, E and Janes, J and Harrower, W and Gorrell, J},
title = {Stabilizing selection and mitochondrial heteroplasmy in the Canada lynx (Lynx canadensis).},
journal = {Genome},
volume = {67},
number = {12},
pages = {493-502},
doi = {10.1139/gen-2023-0094},
pmid = {39226612},
issn = {1480-3321},
mesh = {*Lynx/genetics ; Animals ; *Haplotypes ; *DNA, Mitochondrial/genetics ; Heteroplasmy/genetics ; Selection, Genetic ; Polymorphism, Single Nucleotide ; Mitochondria/genetics ; Genome, Mitochondrial ; Phylogeny ; Canada ; },
abstract = {Mitochondrial DNA is commonly used in population genetic studies to investigate spatial structure, intraspecific variation, and phylogenetic relationships. The control region is the most rapidly evolving and largest non-coding region, but its analysis can be complicated by heteroplasmic signals of genome duplication in many mammals, including felids. Here, we describe the presence of heteroplasmy in the control region of Canada lynx (Lynx canadensis) through intra-individual sequence variation. Our results demonstrate multiple haplotypes of varying length in each lynx, resulting from different copy numbers of the repetitive sequence RS-2 and suggest possible heteroplasmic single nucleotide polymorphisms in both repetitive sequences RS-2 and RS-3. Intra-individual variation was only observed in the repetitive sequences while inter-individual variation was detected in the flanking regions outside of the repetitive sequences, indicating that heteroplasmic mutations are restricted to these repeat regions. Although each lynx displayed multiple haplotypes of varying length, we found the most common variant contained three complete copies of the RS-2 repeat unit, suggesting copy number is regulated by stabilizing selection. While genome duplication offers potential for increased diversity, heteroplasmy may lead to a selective advantage or detriment in the face of mitochondrial function and disease, which could have significant implications for wildlife populations experiencing decline (e.g., bottlenecks) as a result of habitat modification or climate change.},
}

*Lynx/genetics
Animals
*Haplotypes
*DNA, Mitochondrial/genetics
Heteroplasmy/genetics
Selection, Genetic
Polymorphism, Single Nucleotide
Mitochondria/genetics
Genome, Mitochondrial
Phylogeny
Canada

@article {pmid39605599,
year = {2024},
author = {Nolbrant, S and Wallace, JL and Ding, J and Zhu, T and Sevetson, JL and Kajtez, J and Baldacci, IA and Corrigan, EK and Hoglin, K and McMullen, R and Schmitz, MT and Breevoort, A and Swope, D and Wu, F and Pavlovic, BJ and Salama, SR and Kirkeby, A and Huang, H and Schaefer, NK and Pollen, AA},
title = {Interspecies Organoids Reveal Human-Specific Molecular Features of Dopaminergic Neuron Development and Vulnerability.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.11.14.623592},
pmid = {39605599},
issn = {2692-8205},
abstract = {The disproportionate expansion of telencephalic structures during human evolution involved tradeoffs that imposed greater connectivity and metabolic demands on midbrain dopaminergic neurons. Despite the central role of dopaminergic neurons in human-enriched disorders, molecular specializations associated with human-specific features and vulnerabilities of the dopaminergic system remain unexplored. Here, we establish a phylogeny-in-a-dish approach to examine gene regulatory evolution by differentiating pools of human, chimpanzee, orangutan, and macaque pluripotent stem cells into ventral midbrain organoids capable of forming long-range projections, spontaneous activity, and dopamine release. We identify human-specific gene expression changes related to axonal transport of mitochondria and reactive oxygen species buffering and candidate cis- and trans -regulatory mechanisms underlying gene expression divergence. Our findings are consistent with a model of evolved neuroprotection in response to tradeoffs related to brain expansion and could contribute to the discovery of therapeutic targets and strategies for treating disorders involving the dopaminergic system.},
}

@article {pmid39604839,
year = {2024},
author = {Liao, R and Yao, J and Zhang, Y and Liu, Y and Pan, H and Han, B and Song, C},
title = {MYB transcription factors in Peucedanum Praeruptorum Dunn: the diverse roles of the R2R3-MYB subfamily in mediating coumarin biosynthesis.},
journal = {BMC plant biology},
volume = {24},
number = {1},
pages = {1135},
pmid = {39604839},
issn = {1471-2229},
support = {2023YFC3503804//National Key R&D Program of China/ ; TCMRPSU-2022-04//Open Fund of Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resource/ ; TCMADM-2023-03//Open Fund of the Anhui Dabieshan Academy of Traditional Chinese Medicine/ ; },
mesh = {*Transcription Factors/metabolism/genetics ; *Plant Proteins/genetics/metabolism ; *Apiaceae/genetics/metabolism ; *Phylogeny ; *Coumarins/metabolism ; Gene Expression Regulation, Plant ; Gene Expression Profiling ; },
abstract = {BACKGROUND: The MYB superfamily (v-myb avian myeloblastosis viral oncogene homolog) plays a role in plant growth and development, environmental stress defense, and synthesis of secondary metabolites. Little is known about the regulatory function of MYB genes in Peucedanum praeruptorum Dunn, although many MYB family members, especially R2R3-MYB genes, have been extensively studied in model plants.

RESULTS: A total of 157 R2R3-MYB transcription factors from P. praeruptorum were identified using bioinformatics analysis. Comprehensive analyses including chromosome location, microsynteny, gene structure, conserved motif, phylogenetic tree, and conserved domain were further performed. The length of the 157 transcription factors ranged from 120 to 1,688 amino acids (molecular weight between 14.21 and 182.69 kDa). All proteins were hydrophilic. Subcellular localization predictions showed that 155 PpMYB proteins were localized in the nucleus, with PpMYB12 and PpMYB157 localized in the chloroplasts and mitochondria, respectively. Ten conserved motifs were identified in the PpMYBs, all of which contained typical MYB domains. Transcriptome analysis identified 47,902 unigenes. Kyoto Encyclopedia of Genes and Genomes analysis revealed 136 pathways, of which 524 genes were associated with the phenylpropanoid pathway. Differential expressed genes (DEGs) before and after bolting showed that 11 genes were enriched in the phenylpropanoid pathway. Moreover, the expression patterns of transcription genes were further verified by qRT-PCR. With high-performance liquid chromatography (HPLC), 8 coumarins were quantified from the root, stem, and leaf tissue samples of P. praeruptorum at different stages. Praeruptorin A was found in both roots and leaves before bolting, whereas praeruptorin B was mainly concentrated in the roots, and the content of both decreased in the roots and stems after bolting. Praeruptorin E content was highest in the leaves and increased with plant growth. The correlation analysis between transcription factors and coumarin content showed that the expression patterns of PpMYB3 and PpMYB103 in roots align with the accumulation trends of praeruptorin A, praeruptorin B, praeruptorin E, scopoletin, and isoscopoletin, which declined in content after bolting, suggesting that these genes may positively regulate the biosynthesis of coumarins. Eleven distinct metabolites and 48 DEGs were identified. Correlation analysis revealed that the expression of all DEGs were significantly related to the accumulation of coumarin metabolites, indicating that these genes are involved in the regulation of coumarin biosynthesis.

CONCLUSIONS: R2R3-MYB transcription factors may be involved in the synthesis of coumarin. Our findings provide basic data and a rationale for future an in-depth studies on the role of R2R3-MYB transcription factors in the growth and regulation of coumarin synthesis.},
}

*Transcription Factors/metabolism/genetics
*Plant Proteins/genetics/metabolism
*Apiaceae/genetics/metabolism
*Phylogeny
*Coumarins/metabolism
Gene Expression Regulation, Plant
Gene Expression Profiling