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The jaguar (Panthera onca) is the largest living cat species native to the Americas and one of few large American carnivorans to have survived into the Holocene. However, the extent to which jaguar diversity declined during the end-Pleistocene extinction event remains unclear. For example, Pleistocene jaguar fossils from North America are notably larger than the average extant jaguar, leading to hypotheses that jaguars from this continent represent a now-extinct subspecies (Panthera onca augusta) or species (Panthera augusta). Here, we used a hybridization capture approach to recover an ancient mitochondrial genome from a large, late Pleistocene jaguar from Kingston Saltpeter Cave, Georgia, United States, which we sequenced to 26-fold coverage. We then estimated the evolutionary relationship between the ancient jaguar mitogenome and those from other extinct and living large felids, including multiple jaguars sampled across the species' current range. The ancient mitogenome falls within the diversity of living jaguars. All sampled jaguar mitogenomes share a common mitochondrial ancestor ~400 thousand years ago, indicating that the lineage represented by the ancient specimen dispersed into North America from the south at least once during the late Pleistocene. While genomic data from additional and older specimens will continue to improve understanding of Pleistocene jaguar diversity in the Americas, our results suggest that this specimen falls within the variation of extant jaguars despite the relatively larger size and geographic location and does not represent a distinct taxon.

Understanding population history and genetic connectivity is important for assessing the long-term viability of populations. The Atlantic surfclam (Spisula solidissima) has historically been subdivided into two subspecies: lesser-known S.s. simitis in the South Atlantic Bight and Gulf of Mexico, and commercially important S.s. solidissima mostly north of Cape Hatteras. Novel populations of the 'southern' S.s. similis subspecies were previously identified far north of their historical range limit. Here, to test a hypothesis of recency and isolation in the North, population samples from Southern New England S..s. similis were compared for the first time to a population sample from Georgia, as well as to S.s. solidissima. Population structure and demographic history were inferred using genetic variation at a combination of microsatellite, mtDNA, and nuclear intron loci. The Southern New England populations of S.s. similis had slightly lower nuclear DNA diversity than in Georgia. Genetic differentiation between Massachusetts and Georgia S.s. similis was weak and only significant for microsatellite markers. Consistent with weak differentiation, coalescent modeling of nuclear sequence variation indicated high levels of gene flow. All S.s. similis populations had extremely low mtDNA diversity, with only two mitochondrial cytochrome oxidase I haplotypes found in contrast to 15 haplotypes in S.s. solidissima. Collectively, the population genetic patterns are more parsimoniously explained by the northern S.s. similis populations originating from a postglacial expansion rather than recent colonization. KEY WORDS: Spisula solidissima, population structure, gene flow, marine phylogeography, mitochondrial DNA, COI, intron, microsatellites, coalescent model, demographic history, INTRODUCTION It is valuable to assess the population history and genetic connectivity of populations to assess their long-term viability and threat of extinction (Allendorf & Luikart 2009, Hellberg 2009, Nance [...]

Snow leopards (Panthera uncia) inhabit the mountainous regions of High Asia, which experienced serial glacial contraction and expansion during climatic cycles of the Pleistocene. The corresponding impacts of glacial vicariance may have alternately promoted or constrained genetic differentiation to shape the distribution of genetic lineages and population structure. We studied snow leopard phylogeography across High Asia by examining range-wide historical and contemporary genetic structure with mitochondrial DNA and microsatellite markers. We genotyped 182 individuals from across snow leopard range and sequenced portions of the mitogenome in a spatially stratified subset of 80 individuals to infer historical biogeographic and contemporary patterns of genetic diversity. We observed a lack of phylogeographic structure, and analyses suggested a single refugial origin for all sampled populations. Molecular data provided tentative evidence of a hypothesized glacial refugia in the Tian Shan-Pamir-Hindu Kush-Karakoram mountain ranges, and detected mixed signatures of population expansion. Concordant assessments of microsatellite data indicated two global genetic populations, though we detected geographic differences between historical and contemporary population structure and connectivity inferred from mitochondrial and microsatellite data, respectively. Using the largest sample size and geographic coverage to date, we demonstrate novel information on the phylogeographic history of snow leopards, and corroborate existing interpretations of snow leopard connectivity and genetic structure. We recommend that conservation efforts incorporate genetic data to define and protect meaningful conservation units and their underlying genetic diversity, and to maintain the snow leopard's adaptive potential and continued resilience to environmental changes. [ABSTRACT FROM AUTHOR]

Over the last century, Texas has been inundated with exotic ungulates, with as many as 67 species represented by captive and free-ranging populations. One of the most successful species to have established free-ranging populations is the Aoudad (Ammotragus lervia). Herein, we expand on previous genetic studies in Aoudad by including new genomic profiles based on double-digest restriction site-associated DNA sequencing methods with the intent of better understanding the effects of >70 years of human-mediated translocations, population expansion, and gene flow among populations. Using a range of 4,338 to 5,529 single-nucleotide polymorphisms obtained from 73 individuals that potentially represented A. l. blainei , A. l. lervia , and A. l. sahariensis , we measured genetic patterns of diversity and connectivity between source populations from California and New Mexico and resultant aoudad populations in Texas. Principal component analyses identified phylogeographically structured populations across Texas. Further, we identified a signature of isolation by distance among Texas populations. To assess geographic regions that facilitated or blocked gene flow between populations, we used estimation of effective migration surfaces, which indicated 3 barriers to movement between populations as well as connectivity among populations in close proximity. Comparison of mtDNA haplogroups and nuclear genotypes among the 3 examined subspecies were discordant, indicating that the current subspecific taxonomic classification needs refinement. Given the vulnerable status of Aoudad in their native range of northern Africa and the exponential population growth and potential competition with native ungulates in Texas, we propose that efforts to manage non-native Aoudad should strive to maintain and preserve unique genetic units while minimizing competition and other detriments to native species in Texas. Conservation efforts are especially important given the vulnerable status of Aoudad within their native range of northern Africa. [ABSTRACT FROM AUTHOR]

The document from Crustaceana covers a wide range of research articles on various topics related to crustaceans. It includes studies on genetic diversity, population structure, evolutionary transitions, and new species discoveries among different types of crabs and shrimps. The document also delves into the impact of environmental variables on crustacean populations and provides insights into the phylogenetic relationships and reproductive traits of different species. The research presented in the document contributes to a better understanding of crustaceans and their habitats. [Extracted from the article]

The phylogeny of species of Brachyura, particularly within the family Pinnotheridae, remains incompletely understood. To enhance the taxonomy and systematics of the Pinnotheridae, we conducted a comprehensive study aimed at elucidating the phylogenetic position of Arcotheres sinensis. Consequently, we sequenced and annotated the complete mitochondrial genome of A. sinensis , The results revealed that the circular mitogenome of A. sinensis spans 16 520 bp in length. Distinct from typical mitogenomes, A. sinensis contains 13 protein-coding genes (PCGs), 2 ribosomal RNA genes and 23 transfer RNA genes. The A + T content of the A. sinensis mitogenome is 71.63%, with both AT-skew and GC-skew being negative. The lengths of the 23 tRNA genes range from 62 to 72 bp. All tRNA genes exhibit typical cloverleaf structures, except for the trnS1 gene, which lacks the dihydrouridine (DHU) arm. Selection pressure analysis revealed that all PCGs are under evolutionary selection, with cox1 experiencing strongest purifying selection and atp8 undergoing weakest purifying selection. Compared to ancestral Brachyura, the gene order of A. sinensis has been rearranged from R - N - S 1 - E to S 1 - E - N - R and the sequence I - Q - M has transitioned to Q - I - M. Phylogenetic analysis unequivocally positions A. sinensis within the taxonomic framework of the family Pinnotheridae, highlighting its intimate phylogenetic relationship with congeners within the same familial clade, notably Arcotheres purpureus and Pinnotheres excussus. These findings contribute to a better understanding of the status and evolutionary history of Pinnotheridae species. [ABSTRACT FROM AUTHOR]

Objective: Mitochondrial DNA (mtDNA) depletion/deletions syndrome (MDDS) comprises a group of diseases caused by primary autosomal defects of mtDNA maintenance. Our objective was to study the etiology of MDDS in 4 patients who lack pathogenic variants in known genetic causes. Methods: Whole exome sequencing of the probands was performed to identify pathogenic variants. We validated the mitochondrial defect by analyzing mtDNA, mitochondrial dNTP pools, respiratory chain activities, and GUK1 activity. To confirm pathogenicity of GUK1 deficiency, we expressed 2 GUK1 isoforms in patient cells. Results: We identified biallelic GUK1 pathogenic variants in all 4 probands who presented with ptosis, ophthalmoparesis, and myopathic proximal limb weakness, as well as variable hepatopathy and altered T‐lymphocyte profiles. Muscle biopsies from all probands showed mtDNA depletion, deletions, or both, as well as reduced activities of mitochondrial respiratory chain enzymes. GUK1 encodes guanylate kinase, originally identified as a cytosolic enzyme. Long and short isoforms of GUK1 exist. We observed that the long isoform is intramitochondrial and the short is cytosolic. In probands' fibroblasts, we noted decreased GUK1 activity causing unbalanced mitochondrial dNTP pools and mtDNA depletion in both replicating and quiescent fibroblasts indicating that GUK1 deficiency impairs de novo and salvage nucleotide pathways. Proband fibroblasts treated with deoxyguanosine and/or forodesine, a purine phosphatase inhibitor, ameliorated mtDNA depletion, indicating potential pharmacological therapies. Interpretation: Primary GUK1 deficiency is a new and potentially treatable cause of MDDS. The cytosolic isoform of GUK1 may contribute to the T‐lymphocyte abnormality, which has not been observed in other MDDS disorders. ANN NEUROL 2024;96:1209–1224 [ABSTRACT FROM AUTHOR]

The article in JCO Precision Oncology discusses a rare case of metastatic renal oncocytoma in a 29-year-old female patient who showed an exceptional response to treatment. The patient underwent systemic therapy followed by radical nephrectomy and hepatic metastasectomy. Genetic analysis revealed specific alterations in mitochondrial genome copy number, targeted cancer gene mutations, and RNA expression. The study highlights the challenges in diagnosing and treating metastatic renal oncocytoma and provides insights into the genetic and molecular characteristics of this rare condition. [Extracted from the article]

Mating between species occurs within many insect orders. The result of heterospecific mating depends upon the effectiveness of pre‐ and post‐reproductive barriers. Incomplete reproductive barriers lead to introgression of DNA into one species or both. Intricate genital morphology among dragonflies provides little assurance of species specificity given that heterospecific mating or mating attempts have been observed among many species. The genetic consequence is unknown for many heterospecific matings. For example, Somatochlora species mating and genetic exchange have been hypothesized based on observational records and individuals with hybrid morphology. We investigate the potential of heterospecific mating between North American Somatochlora species as inferred from multi‐gene phylogenies. We used mitochondrial genes (COI and ND3) and nuclear genes (EF1‐α and ITS2) to construct phylogenies using maximum parsimony. Observation of non‐monophyletic mtDNA lineages but monophyletic nDNA lineages between Somatochlora sister‐species would indicate mtDNA introgression and suggest heterospecific matings. Our results highlighted three instances of non‐monophyly of mtDNA clades in the following groups: (i) S. hineana + S. tenebrosa; (ii) S. kennedyi + S. forcipata + S. franklini; and (iii) S. calverti + S. provocans + S. filosa. Analysis of partitioned Bremer support indicates that mtDNA COI largely contributed to the non‐monophyly of these species, thus suggesting mtDNA introgression resulting from heterospecific matings. Additionally, the topology resulting from the combined data analysis was concordant with previous taxonomic understanding of Somatochlora species groups. These multi‐gene phylogenies of North American Somatochlora are the first, providing a foundation for future ecological and evolution studies and knowledge for effective decision‐making and public policy, which is especially important for the endangered species, S. hineana. [ABSTRACT FROM AUTHOR]

BACKGROUND: Crustaceans of the superfamily Penaeoidea (e.g., shrimps and prawns) are among the most commercially available aquatic products worldwide. However, there are few studies regarding not only the presence but also the characteristics of mislabelling in these food products. Such information would be helpful for consumers in order to avoid the typical problems associated with mislabelling (e.g., health and economic issues). For this reason, this work considers Penaeoidea mislabelling by comparing different products (frozen, fresh, boiled), and sources (hypermarkets, supermarkets and fishmongers) from Spain (Europe). RESULTS: A total of 94 samples from 55 different products were collected, representing 19 different species from 13 genera. Mitochondrial DNA (COI gene) was amplified, revealing mislabelling in almost 30% of supermarket products and almost exclusively found in frozen samples (95% of the total) regardless of its price. In addition, products from the Pacific Ocean seem to be particularly susceptible to mislabelling. CONCLUSIONS: All in all, recommendations for the consumer in order to avoid mislabelling of prawns include purchasing them fresh from fishmongers; aquaculture products must not be avoided. This study represents, to our knowledge, the first attempt to provide recommendations to consumers based on DNA analyses in order to avoid mislabelling in food products. Further research is therefore required to provide such recommendations in different food products, particularly those that are processed, packaged and/or frozen. © 2024 The Author(s). Journal of the Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

Mitochondrial diseases (MtDs) present diverse clinical phenotypes, yet large‐scale studies are hindered by their rarity. This retrospective, multicenter study, conducted across five Chinese hospitals' neurology departments from 2009 to 2019, aimed to address this gap. Nationwide, 1351 patients were enrolled, with a median onset age of 14.0 (18.5) years. The predominant phenotype was mitochondrial encephalomyopathy, lactic acidosis, and stroke‐like episodes (MELAS) (45.0%). Mitochondrial DNA (mtDNA) mutations were prevalent (87.4%), with m.3243A>G being the most common locus (48.7%). Meanwhile, POLG mutations in nuclear DNA (nDNA) accounted for 16.5%. Comparative analysis based on age groups (with a cut‐off at 14 years) revealed the highest prevalence of MELAS, with Leigh syndrome (LS) and chronic progressive external ophthalmoplegia (CPEO) being the second most common phenotypes in junior and senior groups, respectively. Notably, the most commonly mutated nuclear genes varied across age groups. In conclusion, MELAS predominated in this Chinese MtD cohort, underscored by m.3243A>G and POLG as principal mtDNA mutations and pathogenic nuclear genes. The phenotypic and genotypic disparities observed among different age cohorts highlight the complex nature of MtDs. [ABSTRACT FROM AUTHOR]

Multicopy sequences evolve adaptations for increasing their copy number within nuclei. The activities of multicopy sequences under constraints imposed by cellular and organismal selection result in a rich intranuclear ecology in germline cells. Mitochondrial and ribosomal DNA are managed as domestic herds subject to selective breeding by the genes of the single-copy genome. Transposable elements lead a peripatetic existence in which they must continually move to new sites to keep ahead of inactivating mutations at old sites and undergo exponential outbreaks when the production of new copies exceeds the rate of inactivation of old copies. Centromeres become populated by repeats that do little harm. Organisms with late sequestration of germ cells tend to evolve more "junk" in their genomes than organisms with early sequestration of germ cells. [ABSTRACT FROM AUTHOR]

Mitochondrial diseases are distinct types of metabolic and/or neurologic abnormalities that occur as a consequence of dysfunction in oxidative phosphorylation, affecting several systems in the body. There is no effective treatment modality for mitochondrial disorders so far, emphasizing the clinical significance of preventing the inheritance of these disorders. Various reproductive options are available to reduce the probability of inheriting mitochondrial disorders, including in vitro fertilization (IVF) using donated oocytes, preimplantation genetic testing (PGT), and prenatal diagnosis (PND), among which PGT not only makes it possible for families to have genetically-owned children but also PGT has the advantage that couples do not have to decide to terminate the pregnancy if a mutation is detected in the fetus. PGT for mitochondrial diseases originating from nuclear DNA includes analyzing the nuclear genome for the presence or absence of corresponding mutations. However, PGT for mitochondrial disorders arising from mutations in mitochondrial DNA (mtDNA) is more intricate, due to the specific characteristics of mtDNA such as multicopy nature, heteroplasmy phenomenon, and exclusive maternal inheritance. Therefore, the present review aims to discuss the utility and challenges of PGT as a preventive approach to inherited mitochondrial diseases caused by mtDNA mutations. [ABSTRACT FROM AUTHOR]

The effect of pachymic acid (PA) on pulmonary fibrosis in rats was expected to be investigated in this study. Firstly, bleomycin (BLM) was used to establish pulmonary fibrosis rat model, then PA (10, 20, or 40 mg/kg) was intragastrically administered to the rats for 14 days. Subsequently, a variety of tests was performed to observe changes in sample tissues after different treatments. Briefly, the degree of pulmonary edema in rats was assessed through dry/wet weight ratio. Hematoxylin and eosin (H&E) staining and Masson's trichrome staining were used to observe the pathological injury and fibrosis of lung tissue. Biochemical kits were applied to measure the levels of hydroxyproline (Hyp), transforming growth factor beta‐1 (TGFβ‐1), malondialdehyde (MDA), reactive oxygen species (ROS), and adenosine triphosphate (ATP) and the activities of superoxide dismutase (SOD) and catalase (CAT) in rat lung tissues of each group. The mitochondrial DNA (mtDNA) copy number in rat lung tissue was tested using qRT‐PCR. Additionally, the western blot was employed to detect the expression levels of pulmonary fibrosis‐related proteins and endoplasmic reticulum (ER) stress‐related proteins in each group of rat lung tissue. By virtue of experimental verification above, PA was discovered to alleviate BLM‐induced pulmonary edema, pulmonary fibrosis and histopathological damage. On the one hand, PA treatment decreased Hyp and TGF‐β1 levels and down‐regulated pulmonary fibrosis‐related protein expression [collagen I, α‐smooth muscle actin (α‐SMA), and fibronectin] in the lung tissue of BLM rats. On the other hand, it significantly increased the levels of SOD, CAT and ATP while decreased the activities of MDA and ROS in BLM rat lung tissues. In addition, the expression levels of ER stress‐related proteins [glucose‐regulated protein 78 (GRP78), C/EBP homologous protein (CHOP), Caspase 9, and activating transcription factor 4 (ATF4)] were significantly down‐regulated in the lung tissue of BLM rats after PA treatment. Collectively, PA may ameliorate BLM‐induced pulmonary fibrosis and histopathological damage in rats through inhibiting ER stress and improving mitochondrial function. [ABSTRACT FROM AUTHOR]

Mitochondria dysfunction is implicated in cell death, inflammation, and autoimmunity. During viral infections, some viruses employ different strategies to disrupt mitochondria-dependent apoptosis, while others, including SARS-CoV-2, induce host cell apoptosis to facilitate replication and immune system modulation. Given mitochondrial DNAs (mtDNA) role as a pro-inflammatory damage-associated molecular pattern in inflammatory diseases, we examined its levels in the serum of COVID-19 patients and found it to be high relative to levels in healthy donors. Furthermore, comparison of serum protein profiles between healthy individuals and SARS-CoV-2-infected patients revealed unique bands in the COVID-19 patients. Using mass spectroscopy, we identified over 15 proteins, whose levels in the serum of COVID-19 patients were 4- to 780-fold higher. As mtDNA release from the mitochondria is mediated by the oligomeric form of the mitochondrial-gatekeeper—the voltage-dependent anion-selective channel 1 (VDAC1)—we investigated whether SARS-CoV-2 protein alters VDAC1 expression. Among the three selected SARS-CoV-2 proteins, small envelope (E), nucleocapsid (N), and accessory 3b proteins, the E-protein induced VDAC1 overexpression, VDAC1 oligomerization, cell death, and mtDNA release. Additionally, this protein led to mitochondrial dysfunction, as evidenced by increased mitochondrial ROS production and cytosolic Ca2+ levels. These findings suggest that SARS-CoV-2 E-protein induces mitochondrial dysfunction, apoptosis, and mtDNA release via VDAC1 modulation. mtDNA that accumulates in the blood activates the cGAS-STING pathway, triggering inflammatory cytokine and chemokine expression that contribute to the cytokine storm and tissue damage seen in cases of severe COVID-19. [ABSTRACT FROM AUTHOR]

The Phyllidiidae (Gastropoda, Nudibranchia) is a family widely found on coral reefs of tropical waters. To date, their phylogenetic relationships remain controversial at various taxonomic levels. Here we sequenced the complete mitochondrial genomes (mitogenome) of 12 specimens representing nine species from the South China Sea, compared their mitogenomic features and reconstructed the phylogeny of Phyllidiidae. The assembled mitogenomes were 14,543–15,075 bp long containing the typical elements of the 37 genes in the same order. Phylogenetic analysis based on the 13 protein-coding genes revealed that the genera Phyllidia and Phyllidiopsis were closely related, and Phyllidiella was sister to them. Within each genus, inconsistent topology was frequently found between the mitogenomic and morphological trees, cautioning the need for a further integrative taxonomy. The species Phyllidiella pustulosa was proven to be a species complex as three distinctly separated clades appeared. Divergence time estimation dated the origin of the Phyllidiidae at c. 40.33 million years ago (MYA), while the crown ages of the three genera dated back from c. 31.98 to 15.80 MYA, all falling in the period from the Neogene to Paleogene, a time characterized by dramatic climate shifts that might have facilitated species diversification. [ABSTRACT FROM AUTHOR]

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Background: Leber hereditary optic neuropathy (LHON) is a mitochondrial DNA (mtDNA) rare disease due to the pathogenic variant of the NADH dehydrogenase enzyme. LHON is characterized by a sudden central vision loss due to focal degeneration of the retinal ganglion cell layer and optic nerve. Symptoms usually appear between the age of 18 and 35 years. Some individuals present the mtDNA mutations but not presented the LHON clinical features. The heteroplasmic or homoplasmic character of the mutations among patients explains why they develop the disease or not even though they carry the pathogenic variant. Methods: This study was performed in collaboration with the department of ophthalmology of Farhat Hached Hospital, Sousse, Tunisia. Screening for the common mutations in Mt-ND1 gene (m.3460G > A), Mt-ND4 gene (m.11778G > A) and Mt-ND6 gene (m.14484T > C) was performed in five Tunisian families by standard RFLP PCR, followed by direct sequencing of the entire of these genes. Indeed, bioinformatics tools were used to predict the potential functional impact of the identified mutations on the Human mitochondrial respiratory complex I protein. Results: one novel p.L601M (m.1413 C > A) and four previously reported mutations were identified in this study including: rs199476112G > A (m.11778G > A); rs202227543G > A (m.14258G > A); rs1603224763 (m.14510 dup) and NC_012920.1: m.3244G > C. In this present report, only one patient was found carrying the primary point mutation (m. 11778G > A). The ophthalmologic findings showing major fundus changes included hyperemic optic discs; disc pseudo-oedema and microangiopathy leading to optic disc atrophy. The analyses of the stability of protein upon identified mutations using DynaMut tool server demonstrated that these variations induce a rigidification in the region where they are located. Conclusion: This is the first Tunisian report of mtDNA mutations identified in Tunisia causing the LHON. The main factors involved in the pathophysiological mechanisms of this disease are genetic, epigenetic, hormonal and environmental influences. [ABSTRACT FROM AUTHOR]

Aim Methods Results Conclusions In developed nations, women have increasingly deferred childbearing, leading to a rise in demand for infertility treatments and the widespread use of assisted reproductive technologies. However, despite advancements in in vitro fertilization (IVF), live birth rates among women over 40 remain suboptimal. Mitochondrial dysfunction is widely recognized as a key factor in the processes driving the age‐related deterioration in both the quantity and quality of oocytes. We aim to summarize current insights into ovarian aging, with a particular focus on pathways that impair mitochondrial function, and explore directions for future research.Electronic databases were searched for articles published up to June 30, 2024.Ongoing ovulation, luteolysis, and menstruation trigger exogenous reactive oxygen species (ROS)‐mediated oxidative stress that damages mitochondrial DNA. This, in turn, reduces nuclear gene expression, compromises mitochondrial oxidative phosphorylation, and diminishes adenosine 5′ triphosphate production. Persistent endogenous ROS further exacerbate mitochondrial DNA damage and aneuploidy, ultimately causing irreversible chromosomal abnormalities, leading to oocyte aging.We have delineated the pathway from oxidative stress to ovarian aging. Early detection and management of ovarian aging present challenges and opportunities to enhance IVF treatment strategies. [ABSTRACT FROM AUTHOR]

Five stink bugs, Aelia acuminata, A. fieberi, A. furcula, A. klugii and A. sibirica, are found in China and have similar morphologies. Due to the lack of molecular data, the species boundaries and phylogenetic relationships among these five species remain uncertain. In this study, we integrated mitochondrial DNA and nuclear single nucleotide polymorphisms (SNPs) generated by double‐digest restriction site‐associated DNA sequencing (ddRAD‐seq) to perform species delimitation and phylogenetic analyses of the five Aelia species. Most species delimitation analyses based on the cytochrome c oxidase subunit I (COI) gene, mitochondrial genomes and nuclear SNPs yielded five molecular operational taxonomic units (MOTUs), which correspond well to the five Aelia species identified based on morphological characters. We obtained a clear mito‐nuclear discordance between the tree topologies based on mitochondrial genome and genome‐wide SNP data. The D‐statistic and TreeMix analysis suggested that introgression is the most likely cause of mito‐nuclear discordance in Aelia species, which requires confirmation through more extensive sampling and comprehensive data. This study provides the first molecular evidence of the species boundaries and phylogenetic relationships of these five Aelia stink bugs, which is crucial to our understanding of the biodiversity and evolution of Aelia species. [ABSTRACT FROM AUTHOR]

ABSTRACT Mitochondria are dynamic and plastic, undergoing continuous fission and fusion and rearrangement of their bioenergetic sub‐compartments called cristae. These fascinating processes are best understood in animal and fungal models, which are taxonomically grouped together in the expansive Opisthokonta supergroup. In opisthokonts, crista remodelling and inner membrane fusion are linked by dynamin‐related proteins (DRPs). Animal Opa1 (optical atrophy 1) and fungal Mgm1 (mitochondrial genome maintenance 1) are tacitly considered orthologs because their similar mitochondria‐shaping roles are mediated by seemingly shared biochemical properties, and due to their presence in the two major opisthokontan subdivisions, Holozoa and Holomycota, respectively. However, molecular phylogenetics challenges this notion, suggesting that Opa1 and Mgm1 likely had separate, albeit convergent, evolutionary paths. Herein, we illuminate disparities in proteolytic processing, structure, and interaction network that may have bestowed on Opa1 and Mgm1 distinct mechanisms of membrane remodelling. A key disparity is that, unlike Mgm1, Opa1 directly recruits the mitochondrial phospholipid cardiolipin to remodel membranes. The differences outlined herein between the two DRPs could have broader impacts on mitochondrial morphogenesis. Outer and inner membrane fusion are autonomous in animals, which may have freed Opa1 to repurpose its intrinsic activity to remodel cristae, thereby regulating the formation of respiratory chain supercomplexes. More significantly, Opa1‐mediated crista remodelling has emerged as an integral part of cytochrome c‐regulated apoptosis in vertebrates, and perhaps in the cenancestor of animals. By contrast, outer and inner membrane fusion are coupled in budding yeast. Consequently, Mgm1 membrane‐fusion activity is inextricable from its role in the biogenesis of fungal lamellar cristae. These disparate mitochondrial DRPs ultimately may have contributed to the different modes of multicellularity that have evolved within Opisthokonta. [ABSTRACT FROM AUTHOR]

Mitochondrial dysfunction causes devastating disorders, including mitochondrial myopathy, but how muscle senses and adapts to mitochondrial dysfunction is not well understood. Here, we used diverse mouse models of mitochondrial myopathy to show that the signal for mitochondrial dysfunction originates within mitochondria. The mitochondrial proteins OMA1 and DELE1 sensed disruption of the inner mitochondrial membrane and, in response, activated the mitochondrial integrated stress response (mt-ISR) to increase the building blocks for protein synthesis. In the absence of the mt-ISR, protein synthesis in muscle was dysregulated causing protein misfolding, and mice with early-onset mitochondrial myopathy failed to grow and survive. The mt-ISR was similar following disruptions in mtDNA maintenance (Tfam knockout) and mitochondrial protein misfolding (CHCHD10 G58R and S59L knockin) but heterogenous among mitochondria-rich tissues, with broad gene expression changes observed in heart and skeletal muscle and limited changes observed in liver and brown adipose tissue. Taken together, our findings identify that the DELE1 mt-ISR mediates a similar response to diverse forms of mitochondrial stress and is critical for maintaining growth and survival in early-onset mitochondrial myopathy. Synopsis: Mitochondrial myopathies caused by diverse mitochondrial stressors, including mitochondrial DNA (mtDNA) depletion or mitochondrial protein misfolding, activate a similar transcriptional response in muscle. This report shows that this transcriptional response is predominately mediated by the DELE1-dependent mitochondrial integrated stress response (mt-ISR) pathway and is critical for maintaining growth and survival in mouse models. DELE1 is responsible for a protective ISR in response diverse mitochondrial stressors, including mtDNA depletion and mitochondrial protein misfolding. The DELE1-dependent mt-ISR is especially critical for growth and survival in the setting of early-onset mitochondrial stress. DELE1 and OMA1 have overlapping but separable protective effects in mitochondrial myopathies. The DELE1 mt-ISR increases the building blocks for cellular protein synthesis but fails to restore OXPHOS or resolve defects in mitochondrial structure. DELE1 is required to maintain folding of newly synthesized proteins in skeletal muscle under stress. DELE1, a mitochondrial stress signal, protects striated muscle cells by suppressing the misfolding of newly translated proteins. [ABSTRACT FROM AUTHOR]

Mitochondrial DNA (mtDNA) is present in multiple copies within cells and is required for mitochondrial ATP generation. Even within individual cells, mtDNA copies can differ in their sequence, a state known as heteroplasmy. The principles underlying dynamic changes in the degree of heteroplasmy remain incompletely understood, due to the inability to monitor this phenomenon in real time. Here, we employ mtDNA-based fluorescent markers, microfluidics, and automated cell tracking, to follow mtDNA variants in live heteroplasmic yeast populations at the single-cell level. This approach, in combination with direct mtDNA tracking and data-driven mathematical modeling reveals asymmetric partitioning of mtDNA copies during cell division, as well as limited mitochondrial fusion and fission frequencies, as critical driving forces for mtDNA variant segregation. Given that our approach also facilitates assessment of segregation between intact and mutant mtDNA, we anticipate that it will be instrumental in elucidating the mechanisms underlying the purifying selection of mtDNA. Synopsis: The basis for dynamic changes in mitochondria DNA variations in cell populations, known as heteroplasmy, remains unclear. Here, live-cell tracking of mtDNA variants in yeast populations reveals mechanistic principles underlying mtDNA variant segregation. mtDNA variants encoding fluorescent reporters facilitate microscopy approaches for monitoring mtDNA variant segregation in real-time in a dividing yeast population. Asymmetric partitioning of mtDNA copies between mother and daughter cells as well as mitochondrial fission rates determine the rate of mtDNA variant segregation. mtDNA variant segregation is delayed in ∆mrx6 cells with increased mtDNA copy number. The imaging approach allows monitoring of purifying selection against mutant mtDNA. Tracking mtDNA variants in live yeast populations reveals asymmetric partitioning of mtDNA copies during cell division as well as limited mitochondrial fusion/fission frequencies as critical drivers of mtDNA variant segregation. [ABSTRACT FROM AUTHOR]

Quantifying the features of mitochondrial genome structural variation is crucial for understanding its contribution to complexity. Accurate quantification and interpretation of organizational diversity can help uncover biological evolutionary laws and patterns. The current qMGR approach accumulates the changes in two adjacent genes to calculate the rearrangement frequency RF of each single gene and the rearrangement score RS for specific taxa in the mitogenomes of a given taxonomic group. However, it may introduce bias, as it assigns scores to adjacent genes rather than to rearranged genes. To overcome this limitation, we propose a novel statistical method called qGO to quantify the diversity of gene organization. The qGO method, which is based on the homology of gene order, provides a more accurate representation of genome organizational diversity by partitioning gene strings and individually assigning weights to genes spanning different regions. Additionally, a comprehensive approach is employed for distance computation, generating an extensive matrix of rearrangement distances. Through experiments on more than 5500 vertebrate mitochondrial genomes, we demonstrated that the qGO method outperforms existing methods in terms of accuracy and interpretability. This method improves the comparability of genomes and allows a more accurate comparison of the diversity of mitochondrial genome organization across taxa. These findings have significant implications for unraveling genome evolution, exploring genome function, and investigating the process of molecular evolution. [ABSTRACT FROM AUTHOR]

Background Methods Results Conclusions Liver transplantation (LT) is still limited by organ shortage and post‐transplant monitoring issues. While machine perfusion techniques allow for improving organ preservation, biomarkers like donor‐derived cell‐free DNA (dd‐cfDNA) and mitochondrial cfDNA (mt‐cfDNA) may provide insights into graft injury and viability pre‐ and post‐LT.A prospective observational cohort study was conducted on LT recipients (n = 45) to evaluate dd‐cfDNA as a biomarker of graft dysfunction during the first 6 months after LT. Dd‐cfDNA was quantified on blood samples collected pre‐LT and post‐LT using droplet digital PCR. In livers undergoing dual hypothermic oxygenated machine perfusion (D‐HOPE), total cfDNA and mt‐cfDNA levels were measured on perfusate samples collected at 30‐min intervals. Correlations with graft function and clinical outcomes were assessed.Dd‐cfDNA levels peaked post‐LT and correlated with transaminase levels and histological injury severity. The longitudinal assessment showed that postoperative complications and rejection were associated with an increase in dd‐cfDNA levels. Mt‐cfDNA levels in D‐HOPE perfusate correlated with graft function parameters post‐LT and were higher in patients with early allograft dysfunction and severe complications.This study confirms dd‐cfDNA as a marker of graft injury after LT and suggests that perfusate mt‐cfDNA levels during D‐HOPE correlate with graft function and post‐transplant clinical outcome. Integration of these tests into clinical practice may improve transplant management and viability assessment during hypothermic perfusion. [ABSTRACT FROM AUTHOR]

Simple Summary: Genetic methods can currently be used to identify the species of an animal on the basis of the animal itself, its fragments or tissues, or products obtained from it. This study presents typical molecular markers used in species identification. It presents a procedure comparing mtDNA primers used to determine the species of animal from which an item secured at a border crossing (a keychain) was made. Analysis of mitochondrial DNA, specifically the cytochrome b gene (cyt b), has become an essential tool for species identification. In the case of degraded samples, in which DNA is fractionated, universal primers, which are highly effective at amplifying the target region, are necessary. The material analysed in this study was a keychain made of bone, which was secured at a border crossing due to the suspicion that it was made of ivory. Due to processing of the bone and the likelihood of DNA degradation, five pairs of universal primers with different product lengths (from 148 to 990 base pairs) were used for species identification. Fragments of mtDNA from the cyt b and the 12S rRNA and 16S rRNA subunits were analysed. The analysis showed that only one pair of primers (L15601/H15748) enabled identification of the species, which is very common in samples with highly degraded DNA. The material was bone tissue belonging to the species Bos taurus (cattle). Species identification by molecular methods is extremely important in analysis of material when the species cannot be identified on the basis of morphological characteristics. [ABSTRACT FROM AUTHOR]

Comparative analysis based on the mitogenomes of hares in Xinjiang, China, is limited. In this study, the complete mitochondrial genomes of seven hare samples including four hare species and their hybrids from different environments were sequenced, assembled, and annotated. Subsequently, we performed base content and bias analysis, tRNA analysis, phylogenetic analysis, and amino acid sequence analysis of the annotated genes to understand their characteristics and phylogenetic relationship. Their mitogenomes are circular molecules (from 16,691 to 17,598 bp) containing 13 protein-coding genes, two rRNA genes, 22 tRNA genes, and a control region, which are similar with other Lepus spp. worldwide. The relative synonymous codon usage analysis revealed that the adaptation of Lepus yarkandensis to its unique arid and hot environment might be associated with synthesizing amino acids like alanine, leucine, serine, arginine, and isoleucine and the terminator caused by the different usage of codons. Further, we utilized the MEME model and identified two positive selection genes (ND4, ND5) in Lepus tibetanus pamirensis and one (ND5) in L. yarkandensis that might be important to their adaptation to the plateau and dry and hot basin environments, respectively. Meanwhile, Lepus tolai lehmanni and Lepus timidus may have evolved different adaptive mechanisms for the same cold environment. This study explored the evolutionary dynamics of Xinjiang hares' mitochondrial genomes, providing significant support for future research into their adaptation mechanisms in extreme environments. [ABSTRACT FROM AUTHOR]

Ageing is a major risk factor that contributes to increased mortality and morbidity rates during influenza A virus (IAV) infections. Macrophages are crucial players in the defense against viral infections and display impaired function during ageing. However, the impact of ageing on macrophage function in response to an IAV infection remains unclear and offers potential insight for underlying mechanisms. In this study, we investigated the immune response of young and aged human monocyte-derived macrophages to two different H1N1 IAV strains. Interestingly, macrophages of aged individuals showed a lower interferon response to IAV infection, resulting in increased viral load. Transcriptomic data revealed a reduced expression of stimulator of interferon genes (STING) in aged macrophages albeit the cGAS-STING pathway was upregulated. Our data clearly indicate the importance of STING signaling for interferon production by applying a THP-1 STING knockout model. Evaluation of mitochondrial function during IAV infection revealed the release of mitochondrial DNA to be the activator of cGAS-STING pathway. The subsequent induction of apoptosis was attenuated in aged macrophages due to decreased STING signaling. Our study provides new insights into molecular mechanisms underlying age-related immune impairment. To our best knowledge, we are the first to discover an age-dependent difference in gene expression of STING on a transcriptional level in human monocyte-derived macrophages possibly leading to a diminished interferon production. [ABSTRACT FROM AUTHOR]

The over 4,100 species of bird lice are classified into 214 genera in the parvorders Amblycera and Ischnocera. Congeneric species of bird lice usually share much similarity in morphology and in mitochondrial (mt) genome organization. Two recent studies, however, reported substantial intra-genus variation in mt genome organization in bird lice. Both the ancestral single-chromosome mt genome and a fragmented mt genome with two or three minichromosomes were observed in the genera Austromenopon and Laemobothrion. To better understand intra-genus variation in mt genome organization, we sequenced the complete mt genome of the white spoonbill louse Ibidoecus plataleae and compared it with that of the glossy ibis feather louse Ibidoecus bisignatus reported previously. We found that I. plataleae had a fragmented mt genome with 12 minichromosomes; each minichromosome was 2,798 to 3,628 bp in size and had 2 to 6 genes. This is in stark contrast to the mt genome of I. bisignatus, which has all genes on a single chromosome, 14,909 bp in size. This is the most drastic intra-genus variation in mt genome organization observed to date in animals, indicating an unprecedented rapid process of mt genome fragmentation in the genus Ibidoecus. The divergence time between I. plataleae and I. bisignatus is currently unknown but is estimated to be less than 23 million years. Either many minichromosal split events occurred after I. plataleae diverged from I. bisignatus, or one minichromosome splits into multiple minichromosomes in a single event. Sequencing and comparing more Ibidoecusi species will help understand the unusual mt genome fragmentation in this genus. [ABSTRACT FROM AUTHOR]

The Pleidae, or pygmy backswimmers, is a family of aquatic bugs (Hemiptera, Heteroptera, Nepomorpha) containing four genera. Here, we describe Plea cryptica sp. nov. and redescribe its sister species, Plea minutissima Leach, 1817. Whereas the morphological distinction of these closely related species is only possible for males, molecular data clearly separate them. As part of our taxonomic study, we provide comprehensive molecular data including more than 200 DNA barcodes from all over Europe, complete nuclear ribosomal DNA, full mitochondrial genome data, and 3D scans for both species. Furthermore, the same molecular markers are also presented for Neoplea striola (Fieber, 1844). We used Maximum Likelihood (ML) analyses to reconstruct the phylogeny of the Pleidae and Notonectoidea based on available mitogenomic data. Our study represents a successful implementation of the proposed concept of taxonomics, using data from high-throughput sequencing technologies for integrative taxonomic studies, and allowing high confidence for both biodiversity and ecological research. [ABSTRACT FROM AUTHOR]

Background: Primary mitochondrial diseases (PMD) are one of the most common metabolic genetic disorders. They are due to pathogenic variants in the mitochondrial genome (mtDNA) or nuclear genome (nDNA) that impair mitochondrial function and/or structure. We hypothesize that there is overlap between PMD and other genetic diseases that are mimicking PMD. For this reason, we performed a retrospective cohort study. Methods: All individuals with suspected PMD that underwent molecular genetic and genomic investigations were included. Individuals were grouped for comparison: (1) individuals with mtDNA-PMD; (2) individuals with nDNA-PMD; (3) individuals with other genetic diseases mimicking PMD (non-PMD); (4) individuals without a confirmed genetic diagnosis. Results: 297 individuals fulfilled inclusion criteria. The diagnostic yield of molecular genetics and genomic investigations was 31.3%, including 37% for clinical exome sequencing and 15.8% for mitochondrial genome sequencing. We identified 71 individuals with PMD (mtDNA n = 41, nDNA n = 30) and 22 individuals with non-PMD. Adults had higher percentage of mtDNA-PMD compared to children (p-value = 0.00123). There is a statistically significant phenotypic difference between children and adults with PMD. Conclusion: We report a large cohort of individuals with PMD and the diagnostic yield of urine mitochondrial genome sequencing (16.1%). We think liver phenotype might be progressive and should be studied further in PMD. We showed a relationship between non-PMD genes and their indirect effects on mitochondrial machinery. Differentiation of PMD from non-PMD can be achieved using specific phenotypes as there was a statistically significant difference for muscular, cardiac, and ophthalmologic phenotypes, seizures, hearing loss, peripheral neuropathy in PMD group compared to non-PMD group. [ABSTRACT FROM AUTHOR]

The Fasin rainbow fish, scientifically named Melanotaenia fasinensis, is highly prized by aquarium enthusiasts for its vibrant colors and adaptability to artificial aquatic environments. This species is endemic to the karst landscape of the Bird's Head region in Papua, Indonesia, and belongs to the family Melanotaeniidae. Discovered relatively recently in 2010, this species was designated as endangered by the International Union for Conservation of Nature (IUCN) in 2021. However, there is currently insufficient data regarding its phylogenetic position. To address this gap, our study employed next-generation sequencing (NGS) to analyze the entire mitochondrial genome of M. fasinensis. The mitochondrial genome comprises 13 protein-coding genes, 22 transfer RNA genes, and two ribosomal RNA genes, with a total length of 16,731 base pairs. The base composition of the mitogenome revealed percentages of 27.76% adenine (A), 27.34% thymine (T), 16.15% guanine (G), and 28.75% cytosine (C) residues. Our phylogenetic analysis based on sequence data indicated that all species of the Melanotaeniidae family clustered together on the same branch. Furthermore, the intergeneric and interspecific taxonomic positions were explicit and clear. Phylogenetically, Melanotaeniidae were more closely related to the family Isonidae than to the family Atherinomorus. The phylogenetic position of M. fasinensis was relatively basal within the genus Melanotaenia. This study provides valuable molecular insights for further exploration of the phylogeography and evolutionary history of M. fasinensis and other members of the genus Melanotaenia. [ABSTRACT FROM AUTHOR]

Background: Pepper (Capsicum pubescens), one of five domesticated pepper species, has unique characteristics, such as numerous hairs on the epidermis of its leaves and stems, black seeds, and vibrant purple flowers. To date, no studies have reported on the complete assembly of the mitochondrial genome (mitogenome) of C. pubescens. Understanding the mitogenome is crucial for further research on C. pubescens. Results: In our study, we successfully assembled the first mitogenome of C. pubescens, which was assigned the GenBank accession number OP957066. This mitogenome has a length of 454,165 bp and exhibits the typical circular structure observed in most mitogenomes. We annotated a total of 70 genes, including 35 protein-coding genes (PCGs), 30 tRNA genes, 3 rRNA genes, and 2 pseudogenes. Compared to the other three pepper mitogenomes (KJ865409, KJ865410, and MN196478), C. pubescens OP957066 exhibited four unique PCGs (atp4, atp8, mttB, and rps1), while two PCGs (rpl10 and rps3) were absent. Notably, each of the three pepper mitogenomes from C. annuum (KJ865409, KJ865410, and MN196478) experienced the loss of four PCGs (atp4, atp8, mttB, and rps1). To further explore the evolutionary relationships, we reconstructed a phylogenetic tree using the mitogenomes of C. pubescens and fourteen other species. Structural comparison and synteny analysis of the above four pepper mitogenomes revealed that C. pubescens shares high sequence similarity with KJ865409 and that C. pubescens has rearranged with the other three pepper mitogenomes. Interestingly, we observed 72 similar sequences between the mitochondrial and chloroplast genomes, which accounted for 12.60% of the mitogenome, with a total length of 57,207 bp. These sequences encompassed 12 tRNA genes and the rRNA gene (rrn18). Remarkably, selective pressure analysis suggested that the nad5 gene underwent obvious positive selection. Furthermore, a single-base mutation in three genes (nad1, nad2, and nad4) resulted in an amino acid change. Conclusion: This study provides a high-quality mitogenome of pepper, providing valuable molecular data for future investigations into the exchange of genetic information between pepper organelle genomes. [ABSTRACT FROM AUTHOR]

AbstractThe bottlenose dolphin is a widely distributed species found in temperate waters, including the Mediterranean and Black Seas. The Black Sea population is recognized as a distinct subspecies, Tursiops truncatus ponticus, due to genetic and morphological differences. This study analyzed mitochondrial DNA (mtDNA) sequences of 73 bottlenose dolphin samples collected between 1999 and 2016 along the Turkish Black Sea coast, Turkish Straits System (TSS), Aegean, and Mediterranean Seas revealing 14 haplotypes, eight of which are reported here for the first time.The haplotype network shows two main nodes with star-like sub-networks, but no apparent geographic pattern. The lack of geographical groupings of haplotypes indicates the high mobility of the species within the sampled area. The northern Black Sea bottlenose dolphins (NBS) appear to be genetically differentiated from those in the southwestern Black Sea (SBS), Mediterranean, and Atlantic Ocean, but not from the TSS and Aegean Sea populations. Besides, SBS bottlenose dolphins were differentiated only from those in the western Mediterranean (WM) and the Atlantic. Therefore, NBS and SBS bottlenose dolphins should at least be categorized as different populations. However, contrary to some previous studies there was no evidence supporting the classification of Black Sea bottlenose dolphins as a separate subspecies.The TSS differs only from the Atlantic and the Aegean, and functions like a migratory ‘melting pot’ for surrounding populations. Despite the largest sample size, NBS bottlenose dolphins exhibited the lowest haplotype and nucleotide diversity. This low genetic diversity and potential isolation from adjacent populations highlight the need for prioritizing the conservation of NBS bottlenose dolphins. [ABSTRACT FROM AUTHOR]

The role of mitochondria in immunity is increasingly recognized, but it is unclear how variation in mitochondrial DNA (mtDNA) contributes to variable infection outcomes. To quantify the effect of mtDNA variation on humoral and cell-mediated innate immune responses, we utilized a panel of fruit fly Drosophila melanogaster cytoplasmic hybrids (cybrids), where unique mtDNAs (mitotypes) were introgressed into a controlled isogenic nuclear background. We observed substantial heterogeneity in infection outcomes within the cybrid panel upon bacterial, viral and parasitoid infections, driven by the mitotype. One of the mitotypes, mtKSA2 protected against bacterial, parasitoid, and to a lesser extent, viral infections. Enhanced survival was not a result of improved bacterial clearance, suggesting mtKSA2 confers increased disease tolerance. Transcriptome sequencing showed that the mtKSA2 mitotype had an upregulation of genes related to mitochondrial respiration and phagocytosis in uninfected flies. Upon infection, mtKSA2 flies exhibited infection type and duration specific transcriptomic changes. Furthermore, uninfected mtKSA2 larvae showed immune activation of hemocytes (immune cells), increased hemocyte numbers and ROS production, and enhanced encapsulation response against parasitoid wasp eggs and larvae. Our results show that mtDNA variation acts as an immunomodulatory factor in both humoral and cell-mediated innate immunity and that specific mitotypes can provide broad protection against infections. Author summary: The strength of immune response and the disease symptoms vary among individuals even when exposed to the same pathogen. Much of this variation is due to the genes directly involved in adaptive and innate immune pathways. In addition, mitochondria are emerging as one of the factors modulating immune responses. Mitochondria are cellular organelles with their own genome (mtDNA) involved in many important processes, including producing ATP, the energy currency of the cells. mtDNA mutations leading to mitochondrial dysfunction are often considered harmful upon exposure to pathogens. Here, we used a fruit fly model where unique mtDNA variants are placed in a controlled nuclear genomic background to find out how mtDNA shapes infection outcomes upon bacterial, viral and parasitoid infections. We found that mtDNA variation alters the efficiency of immune response and describe a mtDNA variant that confers protection against variety of pathogens. This protection was at least partially caused by enhanced cell-mediated innate immunity, including higher numbers of immune cells prior to and during infection. [ABSTRACT FROM AUTHOR]

The rosefin barb, Enteromius argenteus, as currently described, is a freshwater fish with a distribution that is geographically separated and divided into the northern population in the Kwanza River system in Angola, and the southern population in the Inkomati River system in South Africa and Eswatini. Due to this disjunct distribution pattern, it is likely that the two populations represent distinct species. mtDNA sequence data and detailed examination of morphometric characters revealed considerable genetic (2.8%–3.5%) and morphological differentiation of the two populations, suggesting their recognition as two distinct species. Enteromius crocodilensis is revalidated and redescribed for the southern population that is readily distinguished from E. argenteus by nonoverlapping circumpeduncular scale counts (12–13 vs. 14) and color pattern (presence of a conspicuous dark band along the midline vs. absence of characteristic melanin patterns). Phylogenetic analysis based on mtDNA cytochrome oxidase subunit I (COI) data places both E. argenteus and E. crocodilensis in a well‐supported clade that includes a number of morphologically similar sawfin barb species from southern and central Africa. [ABSTRACT FROM AUTHOR]

AbstractWe sequenced and assembled mitochondrial genomes of three tenthredinid sawflies (Euura poecilonota, E. striata, and Dolerus timidus) using Oxford Nanopore Technologies’ MinION. The Canu assembler produced circular assemblies (23,000–40,000 bp). Still, errors were found in the highly repetitive non-coding control region because of the fragmented DNA which led to no reads spanning the complete control region, preventing its reliable assembly. Based on the non-repetitive coding region’s sequencing coverage, we estimate the lengths of mitochondrial genomes of E. poecilonota, D. timidus, and E. striata to be about 30,000 bp, 31,000 bp, and 37,000 bp and control region to be 15,000 bp, 16,000 bp, and 22,000 bp respectively. All standard bilaterian mitochondrial genes are in the same order and orientation, except trnQ, which is on the minus strand in Euura and the plus strand in Dolerus. Using published tenthredinid genome data, we show that control region lengths are often underestimated. [ABSTRACT FROM AUTHOR]

Opsonization of red blood cells that retain mitochondria (Mito+ RBCs), a feature of systemic lupus erythematosus (SLE), triggers type I interferon (IFN) production in macrophages. We report that monocytes (Mos) co-produce IFN and mature interleukin-1β (mIL-1β) upon Mito+ RBC opsonization. IFN expression depended on cyclic GMP-AMP synthase (cGAS) and RIG-I-like receptors' (RLRs) sensing of Mito+ RBC-derived mitochondrial DNA (mtDNA) and mtRNA, respectively. Interleukin-1β (IL-1β) production was initiated by the RLR antiviral signaling adaptor (MAVS) pathway recognition of Mito+ RBC-derived mtRNA. This led to the cytosolic release of Mo mtDNA, which activated the inflammasome. Importantly, mIL-1β secretion was independent of gasdermin D (GSDMD) and pyroptosis but relied on IFN-inducible myxovirus-resistant protein 1 (MxA), which facilitated the incorporation of mIL-1β into a trans -Golgi network (TGN)-mediated secretory pathway. RBC internalization identified a subset of blood Mo expressing IFN-stimulated genes (ISGs) that released mIL-1β and expanded in SLE patients with active disease. [Display omitted] • Mos co-produce type I IFN and IL-1β upon Mito+ RBC opsonization • IFN and IL-1β expression rely on sensing RBC-derived mtDNA and mtRNA • IL-1β secretion is MxA mediated and independent of GSDMD and pyroptosis • GPA+ blood Mos expressing IFN and IL-1β are expanded in active SLE SLE is an interferonopathy, but blocking IFN does not benefit all patients. Caielli et al. found that SLE monocytes co-produce IFN and IL-1β, a phenotype recapitulated upon in vitro Mito+ RBC opsonization. Cytosolic sensing of mitochondrial nucleic acids induces MxA, which enables IL-1β secretion independently of GSDMD and pyroptosis. [ABSTRACT FROM AUTHOR]

ABSTRACT Cytoplasmic male sterile (CMS) lines play a crucial role in utilization of heterosis in crop plants. However, the mechanism underlying the manipulation of male sterility in cotton by long non‐coding RNA (lncRNA) and brassinosteroids (BRs) remains elusive. Here, using an integrative approach combining lncRNA transcriptomic profiles with virus‐induced gene silencing experiments, we identify a flower bud‐specific lncRNA in the maintainer line 2074B, lncRNA67, negatively modulating with male sterility in upland cotton (Gossypium hirsutum). lncRNA67 positively regulates cytochrome P274B (GhCYP724B), which acted as an eTM (endogenous target mimic) for miR3367. The suppression of GhCYP724B induced symptoms of BR deficiency and male semi‐sterility in upland cotton as well as in tobacco, which resulted from a reduction in the endogenous BR contents. GhCYP724B regulates BRs synthesis by interacting with GhDIM and GhCYP90B, two BRs biosynthesis proteins. Additionally, GhCYP724B suppressed a unique chimeric open reading frame (Aorf27) in 2074A mitochondrial genome. Ectopic expression of Aorf27 in yeast inhibited cellular growth, and over expression of Aorf27 in tobacco showed male sterility. Overall, the results proved that the miR3367–lncRNA67–GhCYP724B module positively regulates male sterility by modulating BRs biosynthesis. The findings uncovered the function of lncRNA67–GhCYP724B in male sterility, providing a new mechanism for understanding male sterility in upland cotton. [ABSTRACT FROM AUTHOR]

Background: Iron–sulfur cluster assembly 2 (ISCA2) deficiency is linked to an autosomal recessive disorder known as multiple mitochondrial dysfunctions syndrome 4 (MMDS4). This disorder is characterized by leukodystrophy and neuroregression. Currently, most of the reported patients are from Saudi Arabia. All these patients carry a homozygous founder variant (NM_194279.2:c.229G>A:p.Gly77Ser) in ISCA2. Methods: We describe a patient who underwent full clinical evaluation, including metabolic, neurological, and radiological examinations. Standard genetic testing, including whole exome sequencing coupled with autozygome analysis, was undertaken, as were assessments of mitochondrial DNA (mtDNA) copy number and mtDNA sequencing on DNA extracted from blood and cultured fibroblasts. Functional workup consisted of splicing assessment of ISCA2 using RT-PCR, biochemical assessment of complex I status using dipstick assays, and mitochondrial respiration measurements using a Seahorse XFp analyzer. Results: We present the clinical and functional characterization of a novel homozygous ISCA2 missense variant (NM_194279.3:c.70A>G:p.Arg24Gly), leading to aberrant splicing in a patient presenting with neuroregression, generalized spasticity with exaggerated deep tendon reflexes and head lag, and progressive loss of acquired milestones. The novel variant was fully segregated in a wider family and was absent in a large control cohort, ethnically matching in-house exomes, local databases such as CGMdb and Saudi Human Genome Program, and ClinVar. Conclusions: Our analyses revealed that the variant is pathogenic, disrupting normal ISCA2 splicing and presumably leading to a truncated protein that disturbs metabolic pathways in patient-derived cells. [ABSTRACT FROM AUTHOR]

Introduction: Banded sheath blight (Bsb) disease, caused by Rhizoctonia solani , is an emerging problem in barnyard millet cultivation. One of the significant goals of pathogenomic research is to identify genes responsible for pathogenicity in the fungus. Methods: A virulence profiling-based approach was employed and six R. solani isolates were collected from various ecological zones of India. The morphological parameters and virulence of all of the six R. solani isolates were investigated. The most virulent strain was designated as RAP2 and its genome has been sequenced, assembled, and annotated. Results: The RAP2 genome is 43.63 megabases in size and comprises 10.95% repetitive DNA, within which 46% are retroelements, 8% are DNA transposons, and 46% are unidentified DNA. The Gene Ontology (GO) annotation of RAP2 proteins revealed that "phosphorylation", "membrane", and "ATP binding" have the highest gene enrichment in the "biological process", "cellular component" and "molecular function" domains, respectively. The genome comprises a majority of secretory proteins in the pectin lyase fold/virulence factor superfamily, which break down plant cell wall polymers to extract saccharides. The RAP2 genome is comparable to R. solani , which infects maize and rice, but it diverges further from soybean in terms of nucleotide-level genetic similarity. Orthologous clustering of RAP2 protein sequences with R. solani infecting maize, rice, and soybean yields 5606 proteins shared across all genomes. GO analysis of 25 proteins specific to the RAP2 genome found enrichment in the ethylene response, which can cause spore germination and infection in host plants. Discussion: Interestingly, a 28-bp deletion in the RAP2 strain's cutinase domain was discovered in the cutinase protein, which might be important in the infection process, perhaps rendering the enzyme inactive or allowing the pathogen to infect barnyard millet while avoiding host defense. This study sheds light on the genetic makeup of R. solani , allowing researchers to discover critical genes related with pathogenicity as well as potential targets for fungicide development. [ABSTRACT FROM AUTHOR]

Background: Astragalus membranaceus (Fisch.) Bunge is one of the most well-known tonic herbs in traditional Chinese medicine, renowned for its remarkable medicinal value in various clinical contexts. The corresponding chloroplast (cp) and nuclear genomes have since been accordingly sequenced, providing valuable information for breeding and phylogeny studies. However, the mitochondrial genome (mitogenome) of A. membranaceus remains unexplored, which hinders comprehensively understanding the evolution of its genome. Results: For this study, we de novo assembled the mitogenome of A. membranaceus (Fisch.) Bunge var. mongholicus (Bunge) P. K. Hsiao using a strategy integrating Illumina and Nanopore sequencing technology and subsequently performed comparative analysis with its close relatives. The mitogenome has a multi-chromosome structure, consisting of two circular chromosomes with a total length of 398,048 bp and an overall GC content of 45.3%. It encodes 54 annotated functional genes, comprising 33 protein-coding genes (PCGs), 18 tRNA genes, and 3 rRNA genes. An investigation of codon usage in the PCGs revealed an obvious preference for codons ending in A or U (T) bases, given their high frequency. RNA editing identified 500 sites in the coding regions of mt PCGs that exhibit a perfect conversion of the base C to U, a process that tends to lead to the conversion of hydrophilic amino acids into hydrophobic amino acids. From the mitogenome analysis, a total of 399 SSRs, 4 tandem repeats, and 77 dispersed repeats were found, indicating that A. membranaceus possesses fewer repeats compared to its close relatives with similarly sized mitogenomes. Selection pressure analysis indicated that most mt PCGs were purifying selection genes, while only five PCGs (ccmB, ccmFc, ccmFn, nad3, and nad9) were positive selection genes. Notably, positive selection emerged as a critical factor in the evolution of ccmB and nad9 in all the pairwise species comparisons, suggesting the extremely critical role of these genes in the evolution of A. membranaceus. Moreover, we inferred that 22 homologous fragments have been transferred from cp to mitochondria (mt), in which 5 cp-derived tRNA genes remain intact in the mitogenome. Further comparative analysis revealed that the syntenic region and mt gene organization are relatively conserved within the provided legumes. The comparison of gene content indicated that the gene composition of Fabaceae mitogenomes differed. Finally, the phylogenetic tree established from analysis is largely congruent with the taxonomic relationships of Fabaceae species and highlights the close relationship between Astragalus and Oxytropis. Conclusions: We provide the first report of the assembled and annotated A. membranaceus mitogenome, which enriches the genetic resources available for the Astragalus genus and lays the foundation for comprehensive exploration of this invaluable medicinal plant. [ABSTRACT FROM AUTHOR]

Two species of Blackwellomyces (Clavicipitaceae, Hypocreales, Ascomycota) were discovered during an investigation of the diversity of entomopathogenic fungi. A new fungus and one known fungal species that were gathered from Yunnan Province were described in this study. Blackwellomyces changningensis, sp. nov. was described using morphology and phylogenetic evidence from 14 mitochondrial protein-coding gene (PCG) data sets (atp6, atp8, atp9, cob, cox1, cox2, cox3, nad1, nad2, nad3, nad4, nad5, nad6, and nad4L) and six nuclear genes (ITS [ITS4 and ITS5], 18S nuc rDNA [18S], 28S nuc rDNA [28S], tef1-α, rpb1, and rpb2). B. changningensis were found parasitic to Lepidoptera larvae and to produce filiform ascospores with septations. The asexual conidia were ovoid to ellipsoid in shape. Phylogenetic analysis and morphological observations concurred that the fungus belonged to a different species within the genus of Blackwellomyces. The foundation for further taxonomic, genetic, and evolutionary biological studies of the genus Blackwellomyces was laid by this work. [ABSTRACT FROM AUTHOR]

Background: Lottiidae (Gray, 1840) is a derived family of Patellogastropoda and an important component of intertidal benthic communities. The mitochondrial genome (mitogenome) has been frequently used to analyze the phylogenetic relationships of Patellogastropoda. We used next-generation sequencing (NGS) to sequence the complete mitogenomes of five species. We analyzed the basic base composition characteristics of these mitogenomes, constructed a phylogenetic tree, compared the characteristics of gene rearrangement with other related species, and discussed the evolutionary patterns between gastropod species and the evolutionary relationships of each subclass. In addition, we aim to infer the differentiation time and evolutionary characteristics of various species in the order Patellogastropoda. These results will enrich the mitogenome database of Patellogastropoda and enhance our understanding of the genetic characteristics of Lottiidae and the phylogenetic relationships between gastropods. Results: We obtained the mitogenomes sequences of Lottia peitaihoensis, Patelloida saccharinoides, Patelloida ryukyuensis, Nipponacmea sp. and Nipponacmea nigrans, using next-generation sequencing technology. We analyzed the basic structural characteristics of their mitogenomes and found that their lengths ranged from 16.6 kbp to 19.1 kbp. While N. nigrans and P. saccharinoides contain 39 genes, L. peitaihoensis, P. ryukyuensis, and Nipponacmea sp. have only 38 genes, with one trnW less. The most abundant base among the five species is T, and most protein coding genes (PCGs) use ATT, ATG, and ATA as starting codons, and TAA and TAG as stopping codons. We selected the mitogenomes of 10 Lottiidae species for selection pressure analysis and found that all PCGs were subject to purifying selection. Phylogenetic analysis indicates that Patellogastropoda is a fundamental branch of the Gastropoda, and Lottiidae, within Patellogastropoda, is an independent branch at the outermost of the entire phylogenetic tree. Comparison of mitochondrial gene sequences of all Patellogastropoda species revealed a high degree of gene rearrangement within the family Lottiidae, eight sequences present among the 10 species examined. By estimating their divergence times, we found that the divergence of limpets occurred as early as the Permian period of the Paleozoic Era, and a large number of species diverged in the Cenozoic Era. Conclusion: The data obtained from this study will provide information on the assembly of the mitochondrial genome of the Lottiidae species, which will contribute to a better understanding of the evolutionary status and relationship among thes family of Patellogastropoda. [ABSTRACT FROM AUTHOR]

Background: Post-intensive care syndrome (PICS) poses a notable public health concern, with survivors of critical illness experiencing long-term physical, psychological, and cognitive challenges. Mitochondrial dysfunction has gained attention for its potential involvement in PICS. However, the long-term impact of mitochondrial status on patient recovery remains uncertain. A single-centre retrospective analysis was conducted in Leeuwarden, the Netherlands, between May and November 2019, within a mixed ICU survivor cohort. Patients were assessed for mitochondrial markers (mtDNA damage represented by the presence of mtDNA fragmentation and mitochondrial DNA levels evaluated by the ratio of mtDNA and nuclear DNA), clinical factors, and long-term outcomes measured by the physical functioning (PF) domain of health-related quality of life. Results: A total of 43 patients were included in this study divided into recovery and non-recovery groups based on age-adjusted PF scores at 12 months post-ICU. Nineteen patients scored below these thresholds. No significant differences in mitochondrial markers between groups were identified. Furthermore, no significant correlations were found between mtDNA levels and mtDNA damage at baseline and 12 months with PF scores. However, mtDNA levels decreased over time in the recovery (p-value < < 0.01) and non-recovery groups (p-value < 0.01). Conclusion: No significant correlation was found between mitochondrial markers and physical functioning scores. This study underscores the multifactorial nature of PICS and the need for a comprehensive understanding of its metabolic and cellular components. While mitochondrial markers may play a role in PICS, they operate within a framework influenced by various factors. This exploratory study serves as a foundation for future investigations aimed at developing targeted interventions to enhance the quality of life for ICU survivors grappling with PICS. [ABSTRACT FROM AUTHOR]

Leber's hereditary optic neuropathy (LHON), a maternally inherited ocular disease, is predominantly caused by mitochondrial DNA (mtDNA) mutations. Mitochondrial tRNA variants are hypothesized to amplify the pathogenic impact of three primary mutations. However, the exact mechanisms remained unclear. In the present study, the synergistic effect of the tRNAGlu 14693A > G and ND6 14484T > C mutations in three Chinese families affected by LHON is investigated. The m.14693A > G mutation nearly abolishes the pseudouridinylation at position 55 of tRNAGlu, leading to structural abnormalities, decreased stability, aberrant mitochondrial protein synthesis, and increased autophagy. In contrast, the ND6 14484T > C mutation predominantly impairs complex I function, resulting in heightened apoptosis and virtually no induction of mitochondrial autophagy compared to control cell lines. The presence of dual mutations in the same cell lines exhibited a coexistence of both upregulated cellular stress responses to mitochondrial damage, indicating a scenario of autophagy and mutation dysregulation within these dual‐mutant cell lines. The data proposes a novel hypothesis that mitochondrial tRNA gene mutations generally lead to increased mitochondrial autophagy, while mutations in genes encoding mitochondrial proteins typically induce apoptosis, shedding light on the intricate interplay between different genetic factors in the manifestation of LHON. [ABSTRACT FROM AUTHOR]

ABSTRACT Background Methods and Results Conclusion The mitochondrial contact site and cristae organising system (MICOS) complex is required for cristae formation and is composed of seven proteins. Among the genes of MICOS complex, variants of MICOS13, IMMT and APOO have been reported to cause diseases.We report a case in which whole genome sequencing identified a variant of the MICOS10 gene associated with mitochondrial hepatopathy along with mitochondrial DNA depletion. We identified the deletion g.19596826_19601303del and the single nucleotide variant c.173G>C (p.Cys58Ser). The deletion including exon 1 might have caused complete loss of gene expression, indicating monoallelic expression from RNA sequencing. MIC10 was lost at the protein level in the patient's fibroblasts, and mitochondrial oxygen consumption was impaired. These were restored by overexpression of MICOS10 in the patient's fibroblasts.Taken together, these findings indicate that MICOS10 is a causative gene for hepatopathy and neuropathy, a disease very similar to that associated with MICOS13. [ABSTRACT FROM AUTHOR]

Background Method Results Conclusions Mitochondrial DNA (mtDNA) rearrangements are recognised factors in mitochondrial disorders and ageing, but their involvement in neurodevelopmental disorders, particularly intellectual disability (ID) and autism spectrum disorder (ASD), remains poorly understood. Previous studies have reported mitochondrial dysfunction in individuals with both ID and ASD. The aim of this study was to investigate the prevalence of large‐scale mtDNA rearrangements in ID and ID with comorbid ASD (ID‐ASD).We used mtDNA‐targeted next‐generation sequencing and the MitoSAlt high‐throughput computational pipeline in peripheral blood samples from 76 patients with ID (mean age 52.5 years, 37% female), 59 patients with ID‐ASD (mean age 41.3 years, 46% female) and 32 healthy controls (mean age 42.4 years, 47% female) from Catalonia.The study revealed a high frequency of mtDNA rearrangements in patients with ID, with 10/76 (13.2%) affected individuals. However, the prevalence was significantly lower in patients with ID‐ASD 1/59 (1.7%) and in HC 1/32 (3.1%). Among the mtDNA rearrangements, six were identified as deletions (median size 6937 bp and median heteroplasmy level 2.3%) and six as duplications (median size 10 455 bp and median heteroplasmy level 1.9%). One of the duplications, MT‐ATP6 m.8765‐8793dup (29 bp), was present in four individuals with ID with a median heteroplasmy level of 3.9%.Our results show that mtDNA rearrangements are frequent in patients with ID, but not in those with ID‐ASD, when compared to HC. Additionally, MitoSAlt has demonstrated high sensitivity and accuracy in detecting mtDNA rearrangements, even at very low heteroplasmy levels in blood samples. While the high frequency of mtDNA rearrangements in ID is noteworthy, the role of these rearrangements is currently unclear and needs to be confirmed with further data, particularly in post‐mitotic tissues and through age‐matched control studies. [ABSTRACT FROM AUTHOR]

Salix psammophila , commonly known as the sandlive willow, is a vital shrub species within the Salicaceae family, particularly significant for its ecological role in regions susceptible to desertification and sandy soils. In this study, we assembled the complete S. psammophila mitochondrial genome using Pacbio HiFi third-generation sequencing data. The genome was found to be a typical single circular structure, with a total length of 715,555 bp and a GC content of 44.89%. We annotated 33 unique protein-coding genes (PCGs), which included 24 core mitochondrial genes and 9 variable genes, as well as 18 tRNA genes (5 of which were multicopy genes) and 3 rRNA genes. Comparative analysis of the PCGs from the mitochondrial genomes of S. psammophila , Populus deltoides , Populus simonii , Salix wilsonii , and Salix suchowensis revealed that these genes are relatively conserved within the Salicaceae family, with variability primarily occurring in the ribosomal protein genes. The absence of the rps14 , which encodes a ribosomal protein, may have played a role in the evolution of stress tolerance in Salicaceae plants. Additionally, we identified 232 SSRs, 19 tandem repeat sequences, and 236 dispersed repeat sequences in the S. psammophila mitochondrial genome, with palindromic and forward repeats being the most abundant. The longest palindromic repeat measured 260 bp, while the longest forward repeat was 86,068 bp. Furthermore, 324 potential RNA editing sites were discovered, all involving C-to-U edits, with the nad4 having the highest number of edits. These findings provide valuable insights into the phylogenetic and genetic research of Salicaceae plants. [ABSTRACT FROM AUTHOR]