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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 [...]

The Black-throated Gray Warbler (Setophaga nigrescens) is a migratory songbird with a widespread and continuous distribution in the North American West. Previously published morphological data support the designation of 2 putative subspecies based on subtle differences in plumage and song; however, whether these patterns are clinal or discrete has yet to be determined. Furthermore, given that patterns of morphological variation occur across multiple distinct habitats and geographical boundaries, underlying population genetic structure may be present. To investigate this question and explore the evolutionary history of S. nigrescens, we conducted the first range-wide phylogeographic analysis of this species using genetic (mitochondrial DNA [mtDNA], ND2 gene sequences), morphological (body measurements), and environmental (niche modeling) data. Overall, our results identified 2 major mtDNA clades. One clade occurs east of the Cascade-Sierra ranges throughout the southwestern, Great Basin, and Rocky Mountain regions in North America (Interior clade), while a second widespread clade is comprised of birds that span the Pacific Northwest, and also across the Great Basin and southwest into the Rocky Mountains (Coastal clade). Divergence time estimates suggest a Pleistocene epoch vicariance event. Environmental niche models predict habitat modification and fragmentation from glacial-interglacial cycles, which were frequent over the Pleistocene. Range expansion northwards following the Last Glacial Maximum was identified from neutrality tests and shifts in suitable habitat from the Mid-Holocene to present-day conditions, where both clades arc likely experiencing secondary contact. We found support for nonequivalent environmental niches among both clades based on a spatial analysis of environmental variables, with the Coastal clade showing greater tolerance to both temperate and xeric climatic conditions across the North American West; however, the environmental space occupied by both clades was more similar to each other than expected by chance. High levels of geographic overlap and a lack of discrete patterns in morphology suggest few contemporary reproductive barriers to gene flow. Received 12 July 2023. Accepted 27 February 2024. Key words: gene tree, mitochondrial DNA, morphology, niche divergence, niche modeling, Pleistocene vicariance, subspecies delimitation. La reinita Setophaga nigrescens es un ave canora migratoria con una distribucion amplia y continua en el Oeste Norteamericano. Datos morfologicos previamente publicados apoyan la denominacion de 2 subespecies putativas basadas en diferencias sutiles en plumaje y canto; sin embargo, aun no se determina si esos patrones son cunales o discretos. Ademas, dado que los patrones de variacion morfologica ocurren en multiples habitats separados con limites geograficos definidos, podria estar presente una estructura poblacional genetica subyacente. Para estudiar esta pregunta y explorar la historia evolutiva de 5. nigrescens, condujimos el primer analisis filogenetico de todo el rango de distribucion de esta especie usando datos geneticos (ADN mitocondrial [mtDNA], secuencias geneticas ND2), morfologicos (medidas corporales) y ambientales (modelamiento de nicho). En general, nuestros resultados identificaron 2 ciados mayores de mtDNA. Un ciado se encuentra en las cordilleras Cascade-Sierra hacia el sudoeste y las regiones de Great Bassin y Rocky Mountain en Norte America (ciado Interior), mientras que un segundo ciado se compone de aves que se enceuntran en el Pacifico noroeste, ademas de a traves del Great Bassin y el sudoeste de las Rocky Mountains (ciado Costero). Los tiempos de divergencias estimados sugieren un evento de vicarianza en la epoca del Pleistoceno. Modelos de nicho ambiental predicen una modificacion y fragmentacion del habitat durante ciclos interglaciales, que eran frecuentes en el Pleistoceno. Una expansion de rango hacia el norte a partir del Ultimo Maximo Glacial frie identificada de pruebas de neutralidad y cambios de habitat favorables de condiciones del Holoceno medio a las actuales, donde ambos ciados posiblemente experimentaron contacto secundario. Encontramos apoyo para nichos ambientales no equivalentes entre ambos ciados basados en el analisis especial de variables ambientales, donde el ciado Costero mostro mayor tolerancia tanto a temperatura como a condiciones climaticas xericas a traves del Oeste Norteamericano; sin embargo, el espacio ambiental ocupado por ambos ciados era mas similar entre ellos que lo esperado por el azar. Altos niveles de sobrelapamiento geografico y una falta de patrones discretos morfologicos sugieren pocas barreras reproductivas contemporaneas al flujo genico. Palabras clave: ADN mitocondrial, arbol genetico, delimitacion de subespecies, divergencia de nicho, modelamiento de nicho, morfologia, vicarianza en el Pleistoceno., Evolutionary biologists have long been interested in investigating how historical and contemporary processes have influenced patterns of biodiversity across the globe. In particular, the historical events associated with Pleistocene glaciations [...]

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]

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]

This study evaluates long-read and short-read sequencing for mitochondrial DNA (mtDNA) heteroplasmy detection. 592,315 bootstrapped datasets generated from two single-nucleotide mismatched ultra-deep sequenced mtDNA samples were used to assess basecalling error and accuracy, limit of heteroplasmy detection, and heteroplasmy detection across various coverage depths. Results showed high Phred scores of data with GC-rich sequence bias for long reads. Limit of detection of 12% heteroplasmy was identified, showing strong correlation (R2 ≥ 0.955) with expected heteroplasmy but underreporting tendency of high-level variants. Nanopore sequencing shows potential for direct applicability in mitochondrial diseases diagnostics, but stringent validation processes to ensure diagnostic result quality are required. [ABSTRACT FROM AUTHOR]

The Chinese Grouse (Tetrastes sewerzowi), a rare endemic bird in China, belongs to the Galliformes order and Tetraonidae family. Despite extensive research, subspecies classification remains inadequate, especially in Pingwu, Sichuan. This study sequenced the mitochondrial genome of T. sewerzowi in Wanglang Nature Reserve, Sichuan, analyzed its structural features, and reconstructed phylogenetic relationships within Tetraonidae. The results indicate that the high conservation in mitochondrial genome structure and sequence between the T. sewerzowi from Wanglang, Sichuan and Lianhuashan, Gansu indicates that they may belong to the same subspecies. Furthermore, we observed significant differences in the length of the mitochondrial control region between T. sewerzowi and Tetrastes bonasia. Based on the phylogenetic tree constructed using a comprehensive mitochondrial dataset, we propose the reclassification of the Hazel Grouse genus into two independent genera: Tetrastes and Bonasa. This study is the first to sequence the mitochondrial genome of T. sewerzowi from Sichuan and compare it with populations from Gansu, providing important insights into the distribution pattern of T. sewerzowi subspecies and facilitating the formulation of effective conservation strategies. [ABSTRACT FROM AUTHOR]

The Hylurgini tribe (Coleoptera: Curculionidae: Scolytinae) comprises commercially significant bark beetles, including invasive species within the genera Dendroctonus and Hylurgus. These invasive species coexist with native Tomicus species of Hylurgini and cooperatively infest host trees in China. However, we lack sufficient mitochondrial genome data of Hylurgini to conduct phylogenetic studies, clarify the phylogenetic relationships of the above species, and improve the understanding of niche divergence and common hazards. Here, we sequenced and analyzed the mitochondrial genomes of seven Hylurgini species, including Dendroctonus valens, Hylurgus ligniperda, Hylurgus micklitzi, Tomicus piniperda, Tomicus brevipilosus, Tomicus minor and Tomicus yunnanensis. All sequenced mitochondrial genomes ranged from 15,339 bp to 17,545 bp in length, and their AT contents ranged from 73.24% to 78.81%. The structure of the seven mitochondrial genomes was consistent with that of ancestral insects. Based on 13 protein-coding genes from the reported mitochondrial genomes of 29 species of bark beetles, we constructed phylogenetic trees using maximum likelihood and Bayesian inference methods. The topology of the two phylogenetic trees was almost consistent. The findings elucidated the taxonomy classification of Hylurgini and the evolutionary connections of its sister taxa within the Scolytinae. This study offers insights for examining the evolutionary connections between invasive and native bark beetles, as well as the molecular identification and detection of newly invading species. [ABSTRACT FROM AUTHOR]

Mitochondrial DNA (mtDNA) variants in patients with myelodysplastic neoplasms (MDS) are shown to be prognostic of outcomes after allogeneic hematopoietic cell transplantation (allo-HCT). However, the prognostic impact of donor mtDNA variants is unknown. Here, we performed whole-genome sequencing on 494 donors who were matched to MDS patients enrolled in the Center for International Blood and Marrow Transplant Research (CIBMTR). We evaluated the impact of donor mtDNA variants on recipients' transplantation outcomes, including overall survival, relapse, relapse-free survival, and transplant-related mortality. The optimism-adjusted bootstrap method was employed to evaluate the prognostic performance of models that include donor mtDNA variants alone and combined with MDS- and HCT-related clinical factors. In the entire donor cohort, we identified 1,825 mtDNA variants, including 67 potential pathogenic variants. Genetic variants on MT-CYB and MT-ND5 genes were identified as independent predictors of posttransplant outcomes. Integration of donor mtDNA variants into the models based on the International Prognostic Scoring System-Revised (IPSS-R) could capture more prognostic information for MDS patients. Sensitivity analysis in 397 unrelated donors obtained similar results. More importantly, we found that incorporating donor mtDNA variants with donor age and the degree of HLA-matching could help to identify "suboptimal" younger HLA-well-matched unrelated donors and "optimal" older HLA-partially/mismatched unrelated donors. Our study shows that mtDNA variants in donors, including those from unrelated donors, hold prognostic value for MDS patients undergoing allo-HCT and augment the prognostic stratification of current scoring systems. These findings present an opportunity to refine donor selection strategies and improve posttransplant outcomes for MDS patients. [ABSTRACT FROM AUTHOR]

Background: Halophila beccarii is one of the oldest two generations of seagrass plants and one of the 10 species of seagrass currently at risk of extinction worldwide. Therefore, how to effectively protect the H. beccarii resources from extinction is a huge challenge. Molecular biology research can provide a scientific basis for species conservation. So far, there has been no detailed analysis of the mitochondrial genome of the genus Halophila. Results: The mitochondrial genome of H. beccarii was assembled into 28 circular chromosomes, ranging in length from 41,738 bp to 104,744 bp, with a total length of 1,964,072 bp and a GC content of 46.71%. It contains 39 genes, including 26 protein coding genes, 10 tRNA genes, and 3 rRNA genes. Repeat sequence analysis and prediction of RNA editing sites revealed a total of 850 dispersed repeats, 1,205 simple repeats, 61 tandem repeats, and 120 RNA editing sites. Analysis of codon usage indicates that codons ending in A/U are preferred. Gene migration between the mitochondrial genome and the chloroplast genome was observed through homologous fragment detection. In addition, Ka/Ks analysis showed that most protein coding genes in the mitochondrial genome experienced negative selection, while only the nad3 gene experienced potential positive selection in most Alismatales. Nucleotide polymorphism analysis revealed variations in each gene, with rpl10 being the most significant. In addition, comparative analysis shows that the GC content is conserved, but there are significant differences in the size and structure of mitochondrial genomes among different species of Alismatales. The phylogenetic analysis based on the mitochondrial genome reflects the exact evolutionary and taxonomic status of H. beccarii. Conclusion: In this study, we sequenced and annotated the mitochondrial genome of H. beccarii, and compared it with the mitochondrial genomes of other plants in Alismatales. Our findings enrich the mitogenome database of seagrass plants and highlight the potential for mitochondrial genes to help decipher plant evolutionary history. [ABSTRACT FROM AUTHOR]

The evolution of independent lineages along replicated environmental transitions frequently results in convergent adaptation, yet the degree to which convergence is present across multiple levels of biological organization is often unclear. Additionally, inherent biases associated with shared ancestry and variation in selective regimes across geographic replicates often pose challenges for confidently identifying patterns of convergence. We investigated a system in which three species of poeciliid fishes sympatrically occur in a toxic spring rich in hydrogen sulfide (H 2 S) and an adjacent nonsulfidic stream to examine patterns of adaptive evolution across levels of biological organization. We found convergence in morphological and physiological traits and genome-wide patterns of gene expression among all three species. In addition, there were shared signatures of selection on genes encoding H 2 S toxicity targets in the mitochondrial genomes of each species. However, analyses of nuclear genomes revealed neither evidence for substantial genomic islands of divergence around genes involved in H 2 S toxicity and detoxification nor substantial congruence of strongly differentiated regions across population pairs. These non-convergent, heterogeneous patterns of genomic divergence may indicate that sulfide tolerance is highly polygenic, with shared allele frequency shifts present at many loci with small effects along the genome. Alternatively, H 2 S tolerance may involve substantial genetic redundancy, with non-convergent, lineage-specific variation at multiple loci along the genome underpinning similar changes in phenotypes and gene expression. Overall, we demonstrate variability in the extent of convergence across organizational levels and highlight the challenges of linking patterns of convergence across scales. [Display omitted] • A novel system with three lineages evolving along the same ecological gradient • Selection from toxic hydrogen sulfide drives trait divergence at small spatial scales • Convergence is evident in morphology, physiology, and the mitochondrial genome • Genomic divergence is characterized by non-convergent, lineage-specific changes Convergent evolution is rarely studied in disparate but sympatric lineages. Greenway et al. study extremophile fishes and find that exposure to the same source of divergent selection results in variable degrees of convergence across different levels of biological organization. [ABSTRACT FROM AUTHOR]

Introduction: With its distinctive evolutionary rate and inheritance patterns separate from the nuclear genome, mitochondrial genome analysis has become a prominent focus of current research. Dendrobium hancockii Rolfe, a species of orchid with both medicinal and horticultural value, will benefit from the application of the fully assembled and annotated mitochondrial genome. This will aid in elucidating its phylogenetic relationships, comparative genomics, and population genetic diversity. Methods: Based on sequencing results from Illumina combined with PacBio and Nanopore, the mitochondrial genome map of D. hancockii was constructed. Comparative analysis was conducted from the perspectives of phylogeny across multiple species, selection pressure on protein-coding genes, and homologous segments. The population diversity of D. hancockii was analyzed using single nucleotide polymorphism (SNP) data from the mitochondrial genome and single-copy nuclear genes. Results and discussion: This research constructed a circular mitochondrial map for D. hancockii , spanning 523,952 bp, containing 40 unique protein-coding genes, 37 transfer RNA genes, and 4 ribosomal RNA genes. Comparative analysis of mitochondrial genes from 26 land plants revealed a conserved gene cluster, " rpl16-ccmFn-rps3-rps19 ," particularly within the Dendrobium genus. The mitochondrial genome of D. hancockii exhibits a lower point mutation rate but significant structural variation. Analysis of 103 resequencing samples identified 19,101 SNP sites, dividing D. hancockii into two major groups with limited gene flow between them, as supported by population diversity, genetic structure analysis, principal component analysis, and phylogenetic trees. The geographical distribution and genetic differentiation of D. hancockii into two major groups suggest a clear phytogeographical division, likely driven by ancient geological or climatic events. The close alignment of mitochondrial data with nuclear gene data highlights the potential of the mitochondrial genome for future studies on genetic evolution in this species. [ABSTRACT FROM AUTHOR]

Eukaryotic energy production requires tight coordination between nuclear and mitochondrial gene products. Because males and females often have different energetic strategies, optimal mitonuclear coordination may be sex-specific. Previous work found evidence for sex-specific mitonuclear effects in the copepod Tigriopus californicus by comparing two parental lines and their reciprocal F1 crosses. However, an alternative hypothesis is that the patterns were driven by the parental source of nuclear alleles. Here, we test this alternative hypothesis by extending the same cross to F2 hybrids, which receive both maternal and paternal nuclear alleles from F1 hybrids. Results confirm mitonuclear effects on sex ratio, with distorted ratios persisting from the F1 to F2 generations, despite reduced fitness in F2 hybrids. No sex-by-cross interactions were found for other phenotypic traits measured. Mitochondrial DNA content was higher in females. Both routine metabolic rate and oxidative DNA damage were lower in F2 hybrids than in parentals. The persistence of sex-specific mitonuclear effects, even in the face of F2 hybrid breakdown, attests to the magnitude of these effects, which contribute to the maintenance of within-population mitochondrial DNA polymorphisms. [ABSTRACT FROM AUTHOR]

Monochamus alternatus is one of the most important borers of conifers and the main vector of the pinewood nematode, Bursaphelenchus xylophilus, the causal agent of pine wilt disease. It causes massive death of pine trees and seriously affects the health of forest ecosystems. Traditionally, adults or larvae are identified by morphological or molecular methods. However, diagnosing M. alternatus larvae at different instars collected from forests is expensive and time‐consuming. Non‐destructive molecular diagnostic protocols are, therefore, being developed to detect biological traces (i.e. exuviae, excreta) and to determine the distribution and spread of this pest. In this study, based on the alignment of mitochondrial DNA cytochrome oxidase subunit I (COI) gene sequences of M. alternatus and other insect species, we designed the primer pair of Mal‐SF/Mal‐SR and probe of Mal‐P for M. alternatus. TaqMan probe‐based qPCR was developed to identify the occurrence of M. alternatus in forests by amplifying the DNA samples obtained from its adult, larva, frass, excreta and exuviae. The amplification results were very effective. The lowest amount of M. alternatus DNA that could be detected with a Cq of 31.93 in the mixed samples was 0.64 pg, showing very high sensitivity. This assay can easily identify M. alternatus from other non‐target wood‐borer species using its frass and exuviae, providing a new diagnostic protocol for monitoring the occurrence and distribution of M. alternatus in forests. [ABSTRACT FROM AUTHOR]

Near the southern limit of its Japanese distribution range, the white-spotted charr Salvelinus leucomaenis inhabits headwater tributaries of inlet rivers to Lake Biwa, Shiga Prefecture, although failing to migrate to the lake from those tributaries. Even though lower depths (>30 m) of the north basin of the lake are cold throughout the year, the only salmonid inhabiting the lake is the Biwa salmon Oncorhynchus sp. However, between 2018 and 2021, five white-spotted charr were caught in Lake Biwa, their phenotype being characterized by large whitish spots, reminiscent of the anadromous form off northern Japan. Mitochondrial DNA Cyt b haplotype analysis data supported their origin as hatchery-reared specimens from Samegai Trout Farm (Shiga Prefecture), the latter having sourced white-spotted charr from several Japanese populations, including northern Japan (descending anadromous exists). Such white-spotted charr, upon release from the hatchery, may have migrated to the lake during winter, due to a retained migration instinct. [ABSTRACT FROM AUTHOR]

The Silver-backed Chevrotain (Tragulus versicolor), a mammal endemic to the unique coastal arid ecosystem in south-central Vietnam, is an enigmatic mouse deer with little information available about its ecology and evolutionary history. The recent rediscovery of the species provides a rare opportunity to clarify its taxonomy and phylogenetic relationship within the genus Tragulus. In this study, we sequenced the complete mitochondrial cytochrome b gene for samples of T. versicolor and T. kanchil from Vietnam. Our molecular results show that the species forms a distinct evolutionary lineage sister to all other species in the genus, confirming the earlier hypothesis based on morphological evidence. However, further research is needed to assess the genetic diversity of the species and design appropriate conservation measures. As the species has not been secured over much of its range, it is recommended that the population in Nui Chua National Park, the only one covered by a protected area, be prioritized for conservation actions. Conserving the species in this unique and imperiled ecosystem will also benefits a suite of locally endemic and threatened species of fauna and flora. [ABSTRACT FROM AUTHOR]

Scoliodon is a genus of small placental sharks living in offshore waters. For a long time, the genus was considered a monotypic genus until a valid species, Scoliodon macrorhynchos, was confirmed in 2010. However, S. muelleri in the same study was not widely recognized because of the lack of evidence. In this study, we obtained the complete mitochondrial genome of the genus Scoliodon from Ranong, Thailand, and tentatively named it Scoliodon sp. By comparing the complete mitochondrial genome with those of two other Scoliodon species and conducting phylogenetic and divergence time analyses, we determined that Scoliodon sp. diverged from the other species. These findings indicate the potential for a new cryptic species (Scoliodon sp.) in the Scoliodon genus. This conclusion was further supported by a subsequent analysis of the published S. laticaudus control region sequences from previous studies. Finally, based on these conclusions, we used machine learning to derive a new identification method for the cryptic species. This approach may be useful for the discovery of new species or cryptic species in other organisms. [ABSTRACT FROM AUTHOR]

African Swine Fever (ASF) is an infectious disease affecting pigs and wild boars, causing significant economic losses. Epidemiological surveillance plays an important role in minimizing its impact. The aim of this study was to evaluate the usefulness of β-actin DNA and mitochondrial DNA (mtDNA) levels in determining the age of animal remains from the Suidae family, which could be helpful in epidemiological investigations. The study included selected tissues and internal organs of Sus scrofa domesticus, exposed to natural environmental conditions or kept in stable 4 °C conditions, to assess the levels of β-actin and mtDNA over a period of 18 months. The levels of both tested parameters exhibited the expected decreasing trend over time. However, in most tissues, some discrepancies from this general pattern were observed. The results obtained for bone marrow showed a consistent downward trend and a strong correlation between mtDNA and β-actin, with long-term detectability (up to the 13th month of the study). Therefore, bone marrow could be considered a matrix of choice for age assessment. However, due to various influencing factors, further studies are required. [ABSTRACT FROM AUTHOR]

Gentiana rigescens, an alpine plant with significant medicinal value, possesses a complex genetic background. However, comprehensive genomic research on G. rigescens is still lacking, particularly concerning its organelle genome. In this study, G. rigescens was studied to sequence the mitochondrial genome (mitogenome) and ascertain the assembly, informational content, and developmental expression of the mitogenome. The mitogenome of G. rigescens was 393,595 bp in length and comprised four circular chromosomes ranging in size from 6646 bp to 362,358 bp. The GC content was 43.73%. The mitogenome featured 30 distinct protein-coding genes, 26 tRNA genes, and 3 rRNA genes. The mitogenome of G. rigescens also revealed 70 SSRs, which were mostly tetra-nucleotides. In addition, 48 homologous fragments were found between the mitogenome and the chloroplast genome, with the longest measuring 23,330 bp. The documentation of the mitochondrial genome of G. rigescens is instrumental in advancing the understanding of its physiological development. Decoding the G. rigescens mitogenome will offer valuable genetic material for phylogenetic research on Gentianaceae and enhance the use of species germplasm resources. [ABSTRACT FROM AUTHOR]

The water lily aphid, Rhopalosiphum nymphaeae, is the only known aphid that can live in both terrestrial and aquatic conditions. In this study, the complete mitochondrial genome of R. nymphaeae was generated using Illumina sequencing technology. The typical circular DNA mitochondrial genome of R. nymphaeae is 15,772 bp in length, with a high A+T content (84.34%). It contains 37 coding genes (13 protein-coding genes, 22 transport RNAs, and two ribosomal RNAs) and two non-coding regions (one control region and one repeat region). Enc-plot, PR2-bias, and neutrality plot analysis indicated that the codon usage of the protein-coding genes is mainly affected by natural selection. The evolution rate analysis (the ratio of nonsynonymous to synonymous, Ka/Ks) indicated that all the PCGs in R. nymphaeae are under a strong purifying selection. The control region has conserved structure elements, and two types of tandem repeat units exist. The length and sequence of the aphid-unique repeat region has high similarity with closely related species. Phylogenetic analyses determined by both maximum likelihood and Bayesian inference support the monophyly of Aphidinae, Aphidini, Aphidina, and Rhopalosiphina. However, the monophyly of the genera in Rhopalosiphina, such as Rhopalosiphum, is still not resolved. This study may help us to understand the phylogenetic relationship of aphids, and much more aphid data are needed in future studies. [ABSTRACT FROM AUTHOR]

[Display omitted] • DNA Plasmodium falciparum glycosylases Pf EndoIII and Pf Ogg1 are targeted to malaria parasite organelles. • Pf EndoIII is a mitochondria-targeted N-glycosylase/AP-lyase. • Ogg1 knockout parasites are impaired in efficient transition from liver to blood stages. • The Plasmodium falciparum mitochondrial genome is an important site for base excision repair. The integrity of genomes of the two crucial organelles of the malaria parasite — an apicoplast and mitochondrion in each cell − must be maintained by DNA repair mediated by proteins targeted to these compartments. We explored the localisation and function of Plasmodium falciparum base excision repair (BER) DNA N-glycosylase homologs Pf EndoIII and Pf Ogg1. These N-glycosylases would putatively recognise DNA lesions prior to the action of apurinic/apyrimidinic (AP)-endonucleases. Both Ape1 and Apn1 endonucleases have earlier been shown to function solely in the parasite mitochondrion. Immunofluorescence localisation showed that Pf EndoIII was exclusively mitochondrial. Pf Ogg1 was not seen clearly in mitochondria when expressed as a Pf Ogg1 leader -GFP fusion, although chromatin immunoprecipitation assays showed that it could interact with both mitochondrial and apicoplast DNA. Recombinant Pf EndoIII functioned as a DNA N-glycosylase as well as an AP-lyase on thymine glycol (Tg) lesions. We further studied the importance of Ogg1 in the malaria life cycle using reverse genetic approaches in Plasmodium berghei. Targeted disruption of Pb Ogg1 resulted in loss of 8-oxo-G specific DNA glycosylase/lyase activity. Pb Ogg1 knockout did not affect blood, mosquito or liver stage development but caused reduced blood stage infection after inoculation of sporozoites in mice. A significant reduction in erythrocyte infectivity by Pb Ogg1 knockout hepatic merozoites was also observed, thus showing that Pb Ogg1 ensures smooth transition from liver to blood stage infection. Our results strengthen the view that the Plasmodium mitochondrial genome is an important site for DNA repair by the BER pathway. [ABSTRACT FROM AUTHOR]

Mitochondrial DNA (mtDNA) mutations are frequent in cancer, yet their precise role in cancer progression remains debated. To functionally evaluate the impact of mtDNA variants on tumor growth and metastasis, we developed an enhanced cytoplasmic hybrid (cybrid) generation protocol and established isogenic human melanoma cybrid lines with wild-type mtDNA or pathogenic mtDNA mutations with partial or complete loss of mitochondrial oxidative function. Cybrids with homoplasmic levels of pathogenic mtDNA reliably established tumors despite dysfunctional oxidative phosphorylation. However, these mtDNA variants disrupted spontaneous metastasis from primary tumors and reduced the abundance of circulating tumor cells. Migration and invasion of tumor cells were reduced, indicating that entry into circulation is a bottleneck for metastasis amid mtDNA dysfunction. Pathogenic mtDNA did not inhibit organ colonization following intravenous injection. In heteroplasmic cybrid tumors, single-cell analyses revealed selection against pathogenic mtDNA during melanoma growth. Collectively, these findings experimentally demonstrate that functional mtDNA is favored during melanoma growth and supports metastatic entry into the blood. [ABSTRACT FROM AUTHOR]

Lung adenocarcinoma is a common aggressive cancer and a leading cause of mortality worldwide. Here, we report an important in vivo role for mitochondrial DNA (mtDNA) copy number during lung adenocarcinoma progression in the mouse. We found that lung tumors induced by KRASG12D expression have increased mtDNA levels and enhanced mitochondrial respiration. To experimentally assess a possible causative role in tumor progression, we induced lung cancer in transgenic mice with a general increase in mtDNA copy number and found that they developed a larger tumor burden, whereas mtDNA depletion in tumor cells reduced tumor growth. Immune cell populations in the lung and cytokine levels in plasma were not affected by increased mtDNA levels. Analyses of large cancer databases indicate that mtDNA copy number is also important in human lung cancer. Our study thus reports experimental evidence for a tumor-intrinsic causative role for mtDNA in lung cancer progression, which could be exploited for development of future cancer therapies. [ABSTRACT FROM AUTHOR]

Cricula trifenestrata Helfer (commonly known as Amphutukoni muga/Cricula silkworm), a wild sericigenous insect produces golden yellow silk similar to Antheraea assamensis (muga silkworm), with significant potential as a natural fiber and biomaterial. Cricula is considered as a pest as it competes for food with muga, which produces the prized golden silk. This study focuses on decoding the mitochondrial genome of C. trifenestrata using next-generation sequencing technology and includes comparative analysis with Bombycoids and other lepidopteran insects. We found that the Cricula mitogenome spans 15 425 bp and exhibits typical gene content and arrangement consistent with other Saturniids and lepidopterans. All protein-coding genes were found to undergo purifying selection, with the highest and lowest conservation observed in the cox1 and atp8 gene, respectively, indicating their potential role in future evolutionary events. We identified two types of mismatches: 23 "G–U" and 6 "U–U" pairs, similar to those found in Actias selene among the Saturniids. Additionally, our study uncovered the presence of two 33 bp repeat units and a "TTAGA" motif in the control region, in contrast to the typical "ATAGA" motif, suggesting functional similarity with evolving sequences. Furthermore, phylogenetic analysis supports the close relationship of Cricula with other species within the Saturniidae family. [ABSTRACT FROM AUTHOR]

SUMMARY: Cytoplasmic male sterility (CMS) is an agronomically significant trait that causes dysfunction in pollen and anther development. It is often observed during successive backcrossing between distantly related species. Here, we show that Asian japonica cultivars (Oryza sativa) exhibit CMS when the nucleus is replaced with that of the African rice Oryza glaberrima. The CMS line produced stunted anthers and did not set any seeds. Mitochondrial orf288 RNA was detected in the anthers of CMS lines but not in fertility restorer lines. The mitochondrial genome‐edited japonica rice that was depleted of orf288 did not exhibit male sterility when backcrossed with O. glaberrima. These results demonstrate that orf288 is a CMS‐causing gene. As orf288 commonly occurs in the mitochondrial genomes of japonica rice, these results indicate that common japonica rice cultivars possess a cryptic CMS‐causing gene hidden in their mitochondrial genomes. [ABSTRACT FROM AUTHOR]

Salmonid fish are known to have the potential to induce allergies. Therefore, from the perspective of food safety, it is crucial to assess the contamination of salmonid components in food. In this study, we aimed to develop a highly sensitive detection method using real-time polymerase chain reaction (PCR) for the accurate identification of minute quantities of salmonid DNA in food. To enhance detection sensitivity, three types of repetitive DNA elements with high copy numbers per genome, that is, the Hpa I element, ribosomal DNA (rDNA), and mitochondrial DNA (mtDNA), were initially selected as candidate PCR targets. The copy numbers of these elements across 11 salmonid species were quantified using real-time PCR. The salmonid-specific retrotransposon with the highest copy number, Hpa I, was chosen as the target gene for the highly sensitive salmonid detection method. By conducting real-time PCR using DNA templates from 11 salmonid species and 71 non-salmonid species, the method demonstrated exceptional specificity to salmonids. By optimizing the conditions of the real-time PCR, the detection limit of salmonid DNA reached 20 fg, and the limit remained unaffected even in the presence of mixed DNA from other species. Compared with existing detection methods for salmonid fish, our approach signifies a substantial 250-fold advancement in detection limits. Application of our method to 16 processed foods containing components of salmonid fish and 5 processed foods devoid of salmonid fish components resulted in successful determination of the presence or absence of salmonid fish in all tested food samples. [ABSTRACT FROM AUTHOR]

Glaucoma is a sight threatening neurodegenerative condition of the optic nerve head associated with ageing and marked by the loss of retinal ganglion cells. Mitochondrial dysfunction plays a crucial role in the pathogenesis of neurodegeneration in the most prevalent type of glaucoma: primary open angle glaucoma (POAG). All previous mitochondrial genome sequencing studies in POAG analyzed mitochondrial DNA (mtDNA) isolated from peripheral blood leukocytes and have not evaluated cells derived from ocular tissue, which better represent the glaucomatous disease context. In this study, we evaluated mitochondrial genome variation and heteroplasmy using massively parallel sequencing of mtDNA in a cohort of patients with POAG, and in a subset assess the role of somatic mitochondrial genome mutations in disease pathogenesis using paired samples of peripheral blood leukocytes and ocular tissue (Tenon's ocular fibroblasts). An enrichment of potentially pathogenic nonsynonymous mtDNA variants was identified in Tenon's ocular fibroblasts from participants with POAG. The absence of oxidative DNA damage and predominance of transition variants support the concept that errors in mtDNA replication represent the predominant mutation mechanism in Tenon's ocular fibroblasts from patients with POAG. Pathogenic somatic mitochondrial genome mutations were observed in people with POAG. This supports the role of somatic mitochondrial genome variants in the etiology of glaucoma. [ABSTRACT FROM AUTHOR]

Mitochondrial genomes are highly conserved in genetic processes and serve as a useful molecular marker for phylogenetic and evolutionary analysis. In this study, the complete mitochondrial genome of Uroobovella oviformis was sequenced and annotated. The mitochondrial genome is a closed, double-stranded circular molecule of 14,306 bp length and contains the typical 37 genes. All of the protein-coding genes started with ATN and terminated with TAA except COX2, COX3, and CYTB, which stopped with single T. The whole mitochondrial genome of U. oviformis showed a heavy AT nucleotide bias (77.69%), a positive AT-Skew (0.035), and a negative GC-Skew (−0.320), as well as translocation of seven genes including CYTB and ND6. The phylogenetic tree was constructed by Bayesian inference and maximum likelihood methods using three different datasets (PCG, PCG12, and AA), which were constructed to discuss the phylogenetic status of Mesostigmata. The analysis showed that the branching relationships among the six trees were consistent and all families except the Laelapidae were recovered as monophyletic. Furthermore, U. oviformis forms a separate clade and is located at the base of Mesostigmata and has a closer relationship with Antennophorina. [ABSTRACT FROM AUTHOR]

Accurate species delimitation and phylogenetic reconstruction are vital to understand biodiversity assessments, conservation management, evolutionary patterns, evolutionary processes, and historical biogeography. The taxonomy and phylogeny of the genus Neolissochilus (Cyprinidae) have a confusing history. We investigated the taxonomy and phylogeny of this group and related lineages using complete mitochondrial genome sequence data from 53 Cyprinidae species and one outgroup species. These analyses show that the monophyly of Neolissochilus and Tor is not supported. N. benasi might represent a new genus, and T. qiaojiensis should be moved into Neolissochilus. We estimated divergence times, evaluated the monophyly of this group, their relationship to other cyprinids, as well as the time course and geography of speciation. The results indicated that the family Cyprinidae likely diverged from other taxa during the Eocene (ca. 54.78 Mya), and species of various genera began to undergo massive diversification events during the Cenozoic Tertiary. The differentiation and diffusion of the family Cyprinidae might be attributed to the Qinghai–Tibet Plateau uplift events, one of the geological events marking the Cenozoic Tertiary period, which cut off genetic exchange between populations through geographic isolation, thus facilitating genetic divergence between populations and eventually leading to the formation of new species. In addition, the results of this study still need further improvement. The limitations are mainly due to the small sample size and the use of only mitochondrial data; therefore, it still needs to be further verified by combining nuclear genome data. [ABSTRACT FROM AUTHOR]

The inference of body fluids and tissues is critical in reconstructing crime scenes and inferring criminal behaviors. Nevertheless, present methods are incompatible with conventional DNA genotyping, and additional testing might result in excessive consumption of forensic scene materials. This study aims to investigate the feasibility of distinguishing common body fluids/tissues through the difference in mitochondrial DNA copy number (mtDNAcn). Four types of body fluids/tissues were analyzed in this study - hair, saliva, semen, and skeletal muscle. MtDNAcn was estimated by dividing the read counts of mitochondrial DNA to that of nuclear DNA (RRmt/nu). Results indicated that there were significant differences in RRmt/nu between different body fluids/tissues. Specifically, hair samples exhibited the highest RRmt/nu (log10RRmt/nu: 4.3 ± 0.28), while semen samples showed the lowest RRmt/nu (log10RRmt/nu: -0.1 ± 0.28). RRmt/nu values for DNA samples without extraction were notably higher (approximately 2.9 times) than those obtained after extraction. However, no significant difference in RRmt/nu was observed between various age and gender groups. Hierarchical clustering and Kmeans clustering analyses showed that body fluids/tissues of the same type clustered closely to each other and could be inferred with high accuracy. In conclusion, this study demonstrated that the simultaneous detection of nuclear and mitochondrial DNA made it possible to perform conventional DNA analyses and body fluid/tissue inference at the same time, thus killing two birds with one stone. Furthermore, mtDNAcn has the potential to serve as a novel and promising biomarker for the identification of body fluids/tissues. [ABSTRACT FROM AUTHOR]

STR loci localized on the X chromosome provide information additional to the autosomal markers routinely analyzed in forensic genetics, integrating genetic systems as Y-STRs and mitochondrial DNA in the investigation of complex kinship scenarios and mass disaster cases. In this study we genotyped 12 X-STR loci in 251 male samples from four populations of Namibia in southern Africa using the Investigator Argus X-12 kit (Qiagen, Hilden, Germany). Forensic efficiency parameters indicated high power of discrimination in the considered populations. As part of our investigation, we highlighted partial linkage associations between loci within known linkage groups (LGs) and identified several occurrences of previously unreported out-of-ladder (OL) alleles. Genetic distances between the Namibian populations here investigated and other African (Eritrea, Ethiopia, Somalia, Guinea, Cape Verde) and non-African (Germany, China, Philippines) populations using loci grouped in LGs mirrored their biogeographical distribution differently for each linkage group. Haplotype sharing within each LG revealed a high degree of population-specific types, hinting to the potential of these markers for ancestry applications. These results highlight the importance to produce specific and freely available population databases especially for multi-ethnic countries. This novel dataset is expected to be of interest for population studies that need an accessible reference dataset of African regions not currently well represented, as well as possible relevance for forensic applications focusing on the biogeographic origin of samples. [ABSTRACT FROM AUTHOR]

Objective: Identify the genotype and clinical characteristics of mitochondrial epilepsy caused by nDNA mutations in Chinese children and explore the treatment and prognosis of the condition. Study design: This is a retrospective cohort study conducted at a single center, including patients diagnosed with an established nDNA mutation-associated primary mitochondrial disease between October 2012 and March 2023 who also met the practical clinical definition of epilepsy published by the ILAE in 2014. Results: Of the 58 patients identified, 74.1% had an onset before the age of 1 year and 63.8% had seizures as their initial symptom. Developmental and epileptic encephalopathy (DEE) (31%) are the most common phenotypes. The most frequently observed MRI abnormalities include abnormal signal asymmetry in the bilateral basal ganglia and/or brainstem (34.7%), as well as brain atrophy, myelin sheath dysplasia, and corpus callosum dysplasia (32.7%). Of the 40 patients followed, seizure treatment was effective in 18 of the cases, while it was ineffective in 22. The mitochondrial DNA depletion syndrome (MDS) was found to be more difficult to control seizures than other phenotypes (P < 0.05). Additionally, the MDS was associated with a significantly higher mortality rate compared to alternative phenotypes (P < 0.05). Conclusions: The onset of mitochondrial epilepsy due to nDNA mutations is early and seizures are the most common initial symptom. DEE is the most common phenotype. Characteristic MRI abnormalities in the brain may be helpful in the diagnosis of primary mitochondrial disease. People with MDS typically face challenges in seizure control and have a poor prognosis. [ABSTRACT FROM AUTHOR]

Parkinson's disease (PD) is a neurodegenerative disorder characterized by the progressive loss of dopaminergic neurons in the substantia nigra pars compacta region of the midbrain and the formation of intracellular protein aggregates known as Lewy bodies, of which a major component is the protein α-synuclein. Several studies have suggested that mitochondria play a central role in the pathogenesis of PD, encompassing both familial and sporadic forms of the disease. Mitochondrial dysfunction is attributed to bioenergetic impairment, increased oxidative stress, damage to mitochondrial DNA, and alteration in mitochondrial morphology. These alterations may contribute to improper functioning of the central nervous system and ultimately lead to neurodegeneration. The perturbation of mitochondrial function makes it a potential target, worthy of exploration for neuroprotective therapies and to improve mitochondrial health in PD. Thus, in the current review, we provide an update on mitochondria-based therapeutic approaches toward α-synucleinopathies in PD. [ABSTRACT FROM AUTHOR]