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Whole genome sequences (WGS) of 185 North American Thoroughbred horses were compared to quantify the number and frequency of variants, diversity of mitotypes, and autosomal runs of homozygosity (ROH). Of the samples, 82 horses were born between 1965 and 1986 (Group 1); the remaining 103, selected to maximize pedigree diversity, were born between 2000 and 2020 (Group 2). Over 14.3 million autosomal variants were identified with 4.5-5.0 million found per horse. Mitochondrial sequences associated the North American Thoroughbreds with 9 of 17 clades previously identified among diverse breeds. Individual coefficients of inbreeding, estimated from ROH, averaged 0.266 (Group 1) and 0.283 (Group 2). When SNP arrays were simulated using subsets of WGS markers, the arrays over-estimated lengths of ROH. WGS-based estimates of inbreeding were highly correlated (r > 0.98) with SNP array-based estimates, but only moderately correlated (r = 0.40) with inbreeding based on 5-generation pedigrees. On average, Group 1 horses had more heterozygous variants (P

Distal sensory polyneuropathy (DSP) and distal neuropathic pain (DNP) remain significant challenges for older people with HIV (PWH), necessitating enhanced clinical attention. HIV and certain antiretroviral therapies (ARTs) can compromise mitochondrial function and impact mitochondrial DNA (mtDNA) replication, which is linked to DSP in ART-treated PWH. This study investigated mtDNA, mitochondrial fission and fusion proteins, and mitochondrial electron transport chain protein changes in the dorsal root ganglions (DRGs) and sural nerves (SuNs) of 11 autopsied PWH. In antemortem standardized assessments, six had no or one sign of DSP, while five exhibited two or more DSP signs. Digital droplet polymerase chain reaction was used to measure mtDNA quantity and the common deletions in isolated DNA. We found lower mtDNA copy numbers in DSP+ donors. SuNs exhibited a higher proportion of mtDNA common deletion than DRGs in both groups. Mitochondrial electron transport chain (ETC) proteins were altered in the DRGs of DSP+ compared to DSP- donors, particularly Complex I. These findings suggest that reduced mtDNA quantity and increased common deletion abundance may contribute to DSP in PWH, indicating diminished mitochondrial activity in the sensory neurons. Accumulated ETC proteins in the DRG imply impaired mitochondrial transport to the sensory neurons distal portion. Identifying molecules to safeguard mitochondrial integrity could aid in treating or preventing HIV-associated peripheral neuropathy.

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]

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]

Upon various stresses, mtDNA leaks from mitochondria into the cytoplasm, leading to cellular dysfunction and inflammation, thereby exacerbating disease progression. The autophagy–lysosome pathway has emerged as a pivotal quality control mechanism for eliminating abnormal cytoplasmic mtDNA. This article summarizes the mechanisms underlying mtDNA-triggered inflammation and how cytoplasmic mtDNA is eliminated. [ABSTRACT FROM AUTHOR]

Mitochondria are unique organelles that have their own genome (mtDNA) and perform various pivotal functions within a cell. Recently, evidence has highlighted the role of mitochondria in the process of stem cell differentiation, including differentiation of neural stem cells (NSCs). Here we studied the importance of mtDNA function in the early differentiation process of NSCs in two cell culture models: the CGR8‐NS cell line that was derived from embryonic stem cells by a lineage selection technique, and primary NSCs that were isolated from embryonic day 14 mouse fetal forebrain. We detected a dramatic increase in mtDNA content upon NSC differentiation to adapt their mtDNA levels to their differentiated state, which was not accompanied by changes in mitochondrial transcription factor A expression. As chemical mtDNA depletion by ethidium bromide failed to generate living ρ° cell lines from both NSC types, we used inhibition of mtDNA polymerase‐γ by 2′‐3′‐dideoxycytidine to reduce mtDNA replication and subsequently cellular mtDNA content. Inhibition of mtDNA replication upon NSC differentiation reduced neurogenesis but not gliogenesis. The mtDNA depletion did not change energy production/consumption or cellular reactive oxygen species (ROS) content in the NSC model used. In conclusion, mtDNA replication is essential for neurogenesis but not gliogenesis in fetal NSCs through as yet unknown mechanisms, which, however, are largely independent of energy/ROS metabolism. [ABSTRACT FROM AUTHOR]

Mitochondria transform the oxygen we breathe and the food we eat to power all brain–body or mind–body processes that produce human experiences. Experimental studies in animals with mitochondrial defects show that mitochondria influence the perception of stressors and/or the resulting psychobiological responses relevant to resilience and aging. Different individuals exhibit qualitative and quantitative differences in their affective, neural, and physiological stress responses; these may in part be explained by interindividual differences in mitochondrial biology, a question not previously examined in humans. The Mitochondrial Stress, Brain Imaging, and Epigenetics (MiSBIE) study includes participants with rare genetic mitochondrial lesions, plus psychobiological stress-response paradigms to examine the mind–mitochondria connection with as much specificity as possible in humans. The MiSBIE dataset and biobank include deep, multivariate phenotyping covering the hallmarks of psychobiology, detailed in the supplemental information online for this article, and data can be requested by the scientific community from the MiSBIE team. Health emerges from coordinated psychobiological processes powered by mitochondrial energy transformation. But how do mitochondria regulate the multisystem responses that shape resilience and disease risk across the lifespan? The Mitochondrial Stress, Brain Imaging, and Epigenetics (MiSBIE) study was established to address this question and determine how mitochondria influence the interconnected neuroendocrine, immune, metabolic, cardiovascular, cognitive, and emotional systems among individuals spanning the spectrum of mitochondrial energy transformation capacity, including participants with rare mitochondrial DNA (mtDNA) lesions causing mitochondrial diseases (MitoDs). This interdisciplinary effort is expected to generate new insights into the pathophysiology of MitoDs, provide a foundation to develop novel biomarkers of human health, and integrate our fragmented knowledge of bioenergetic, brain–body, and mind–mitochondria processes relevant to medicine and public health. [ABSTRACT FROM AUTHOR]

Mitochondria are essential organelles with specialized functions, which play crucial roles in energy production, calcium homeostasis, and programmed cell death. In oocytes, mitochondrial populations are inherited maternally and are vital for developmental competence. Dysfunction in mitochondrial quality control mechanisms can lead to reproductive failure. Due to their central role in oocyte and embryo development, mitochondria have been investigated as potential diagnostic and therapeutic targets in assisted reproduction. Pharmacological agents that target mitochondrial function and show promise in improving assisted reproduction outcomes include antioxidant coenzyme Q10 and mitoquinone, mammalian target of rapamycin signaling pathway inhibitor rapamycin, and nicotinamide mononucleotide. Mitochondrial replacement therapies (MRTs) offer solutions for infertility and mitochondrial disorders. Autologous germline mitochondrial energy transfer initially showed promise but failed to demonstrate significant benefits in clinical trials. Maternal spindle transfer (MST) and pronuclear transfer hold potential for preventing mitochondrial disease transmission and improving oocyte quality. Clinical trials of MST have shown promising outcomes, but larger studies are needed to confirm safety and efficacy. However, ethical and legislative challenges complicate the widespread implementation of MRTs. [ABSTRACT FROM AUTHOR]

Mitochondria are commonly recognized as the powerhouses of the cell, primarily responsible for energy production through oxidative phosphorylation. Alongside this vital function, they also play crucial roles in regulating calcium signaling, maintaining membrane potential, and modulating apoptosis. Their involvement in various cellular pathways becomes particularly evident during oogenesis and embryogenesis, where mitochondrial quantity, morphology, and distribution are tightly controlled. The efficiency of the mitochondrial network is maintained through multiple quality control mechanisms that are essential for reproductive success. These include mitochondrial unfolded protein response, mitochondrial dynamics, and mitophagy. Not surprisingly, mitochondrial dysfunction has been implicated in infertility and ovarian aging, prompting investigation into mitochondria as diagnostic and therapeutic targets in assisted reproduction. To date, mitochondrial DNA copy number in oocytes, cumulus cells, and trophectoderm biopsies, and fluorescent lifetime imaging microscopy-based assessment of NADH and flavin adenine dinucleotide content have been explored as potential predictors of embryo competence, yielding limited success. Despite challenges in the clinical application of mitochondrial diagnostic strategies, these enigmatic organelles have a significant impact on reproduction, and their potential role as diagnostic targets in assisted reproduction is likely to remain an active area of investigation in the foreseeable future. [ABSTRACT FROM AUTHOR]

In this study, we aimed to develop a species-level phylogeny for the Nannospalax genus, identify cryptic species that are difficult to differentiate using standard methods, and further evaluate the relationships across chromosomal forms of several species. 16S rRNA gene sequences from 81 Turkish regions were evaluated and statistical analyzes were conducted. Results are as follows; (i) Nannospalax cilicicus was found to be monophyletic and sister in relation to Nannospalax xanthodon; (ii) We suggested for the first time that the Central-Anatolian populations should be classified under the species name Nannospalax cilicicus (stat. n.); (iii) the unidentified 2n = 52 cytotypes from Bolu and Nannospalax leucodon cytotypes were reciprocally monophyletic, these data support the notion that the 2n = 52 cytotypes from Bolu belong to an unidentified taxon; (iv) study also offered evidence for the monophyly of N. tuncelicus for the first time; (v) Nannospalax xanthodon (2n = 36, 38, and 40) and Nannospalax nehringi composed several species-specific clades, which form polytomy structure, so relationships between these species are still unclear. [ABSTRACT FROM AUTHOR]

The deep-sea raphitomid genus Gymnobela Verrill, 1884 (Neogastropoda: Conoidea) has historically been a container for a multitude of raphitomid species, assigned to this genus almost exclusively based on shell characters. Consequently, the genus has become taxonomically inflated. However, a 2021 molecular study redefined Gymnobela and taxonomically revised the genus. Herein, we present an integrative taxonomic study that, mainly based on samples from Australian waters, further defines this problematic genus, as well as the closely related genus Pontiothauma E.A. Smith, 1895. An automatic barcode gap discovery (ABGD) analysis of three mitochondrial genes resulted in six primary species hypotheses (four in Gymnobela and two in Pontiothauma). We recognised morpho-anatomical and bathymetric/geographical characters distinct to all six and found available names for four; we name one new species, Pontiothauma transregnasp. n., but abstain from naming one presumably unnamed Pontiothauma due to a lack of well-preserved adult specimen material. We provide clear synapomorphic characters unique to both Gymnobela and Pontiothauma, notably those of the radula. Furthermore, we present the first evidence supported by molecular data of a transoceanic distribution among the raphitomids, namely in Gymnobela angulosa Sysoev, 1988. Additionally, we recognise non-molecular evidence that might indicate similarly wide distributions in Gymnobela agasizzi (Verrill and Smith, 1880), Gymnobela engonia Verrill, 1884 and Gymnobela frielei Verrill, 1885. Consequently, and to avoid taxonomic splitting, we herein advocate for wide-ranging investigation of worldwide material when conducting taxonomic studies on deep-sea conoideans, due to growing evidence of transoceanic distributions in the group. Finally, through an exhaustive search of worldwide repositories and the literature, and in conjunction with our molecular, morpho-anatomical and bathymetric/geographical data, we have reassigned 16 species from Gymnobela to other genera within the family Raphitomidae. [ABSTRACT FROM AUTHOR]

As a major energy source for cells, mitochondria are involved in cell growth and proliferation, as well as migration, cell fate decisions, and many other aspects of cellular function. Once thought to be irreparably defective, mitochondrial function in cancer cells has found renewed interest, from suggested potential clinical biomarkers to mitochondria-targeting therapies. Here, we will focus on the effect of mitochondria movement on breast cancer progression. Mitochondria move both within the cell, such as to localize to areas of high energetic need, and between cells, where cells within the stroma have been shown to donate their mitochondria to breast cancer cells via multiple methods including tunneling nanotubes. The donation of mitochondria has been seen to increase the aggressiveness and chemoresistance of breast cancer cells, which has increased recent efforts to uncover the mechanisms of mitochondrial transfer. As metabolism and energetics are gaining attention as clinical targets, a better understanding of mitochondrial function and implications in cancer are required for developing effective, targeted therapeutics for cancer patients. [ABSTRACT FROM AUTHOR]

Genetic connectivity and historical population expansion are characteristics that have largely been studied and observed in several members of the Lutjanidae family throughout the Western South Atlantic, particularly in Brazilian waters. In this study, the population genetic structure of Lutjanus jocu was investigated using four genomic regions: two from mitochondrial DNA (Control Region and Cytochrome B) and two nuclear genes (Delta 6 desaturase—intron 8 and Ribosomal Protein S7—intron 1), in 144 specimens distributed in six locations on the Atlantic coast of Brazil. The results revealed high levels of genetic diversity for both mtDNA and nuDNA markers, and intense gene flow, indicating, consistent with other studies, that this species is represented by a single genetic stock along the Brazilian coast. This is likely due to the high dispersal capacity of L. jocu larvae, driven by the main equatorial currents, as well as biological and ecological factors, contributing to a genetically homogeneous population. Historical demographic analysis and neutrality tests suggest that the species experienced population expansion, possibly during the Pleistocene. Information regarding the genetic structure of populations is extremely important, especially for species of high economic and fishing importance, and can be very useful in guiding stock management and management measures. [ABSTRACT FROM AUTHOR]

Mycobacterium tuberculosis (M. tb) is a significant intracellular pathogen responsible for numerous infectious disease‐related deaths worldwide. It uses ESX‐1 T7SS to damage phagosomes and to enter the cytosol of host cells after phagocytosis. During infection, M. tb and host mitochondria release dsDNA, which activates the CGAS‐STING1 pathway. This pathway leads to the production of type I interferons and proinflammatory cytokines and activates autophagy, which targets and degrades bacteria within autophagosomes. However, the role of type I IFNs in immunity against M. tb is controversial. While previous research has suggested a protective role, recent findings from cgas‐sting1 knockout mouse studies have contradicted this. Additionally, a study using knockout mice and non‐human primate models uncovered a new mechanism by which neutrophils recruited to lung infections form neutrophil extracellular traps. Activating plasmacytoid dendritic cells causes them to produce type I IFNs, which interfere with the function of interstitial macrophages and increase the likelihood of tuberculosis. Notably, M. tb uses its virulence proteins to disrupt the CGAS‐STING1 signaling pathway leading to enhanced pathogenesis. Investigating the CGAS‐STING1 pathway can help develop new ways to fight tuberculosis. [ABSTRACT FROM AUTHOR]

Mitochondria are a unique type of semi-autonomous organelle within the cell that carry out essential functions crucial for the cell's survival and well-being. They are the location where eukaryotic cells carry out energy metabolism. Aside from producing the majority of ATP through oxidative phosphorylation, which provides essential energy for cellular functions, mitochondria also participate in other metabolic processes within the cell, such as the electron transport chain, citric acid cycle, and β-oxidation of fatty acids. Furthermore, mitochondria regulate the production and elimination of ROS, the synthesis of nucleotides and amino acids, the balance of calcium ions, and the process of cell death. Therefore, it is widely accepted that mitochondrial dysfunction is a factor that causes or contributes to the development and advancement of various diseases. These include common systemic diseases, such as aging, diabetes, Parkinson's disease, and cancer, as well as rare metabolic disorders, like Kearns–Sayre syndrome, Leigh disease, and mitochondrial myopathy. This overview outlines the various mechanisms by which mitochondria are involved in numerous illnesses and cellular physiological activities. Additionally, it provides new discoveries regarding the involvement of mitochondria in both disorders and the maintenance of good health. [ABSTRACT FROM AUTHOR]

Currently, the molecular background based on mitochondrial DNA (mtDNA) analysis of canine testicular tumours is underestimated. The available data mostly focus on histopathological evaluations, with a few reports of nuclear genome (nDNA) studies. Tumourigenesis represents a highly complex and diverse genetic disorder, which can also encompass defects in mtDNA. The aim of this study was to identify molecular changes in whole mitochondrial genome sequences obtained from dogs affected by testicular tumours. Samples of blood, tumour, and healthy tissue were collected from each animal, and mtDNA (ultimately 45 samples) was subsequently sequenced. Thereafter, protein analyses were performed to assess the impact of the identified molecular alterations on the amino acid level. The total number of observed changes included 722 SNPs, 12 mutations, 62 indels, 5 indel mutations, and 35 heteroplasmic sites. The highest number of mtDNA variants in protein-coding genes COX1, COX3, ATP6, ND1, ND4, and ND5 was observed. Interestingly, SNPs were found in 10 out of 22 tRNA genes. Most of the identified mtDNA defects were synonymous changes at the amino acid level. Also, polymorphisms and heteroplasmy were frequently observed in the variable number of tandem repeat (VNTR) regions, especially in its fragment spanning 16,138–16,358 bp. Based on the obtained results, it was possible to select 11 polymorphisms that occurred in all the tested samples (benign, malignant) and an additional five SNPs identified only in benign neoplasms. The comprehensive analysis of malignant testicular tumours demonstrated a significant diversity in their molecular profiles, with changes ranging from 17 to 101 per sample. [ABSTRACT FROM AUTHOR]

Summary: The holoparasitic plant Lophophytum mirabile exhibits remarkable levels of mitochondrial horizontal gene transfer (HGT). Gathering comparative data from other individuals and host plants can provide insights into the HGT process.We sequenced the mitochondrial genome (mtDNA) from individuals of two species of Lophophytum and from mimosoid hosts. We applied a stringent phylogenomic approach to elucidate the origin of the whole mtDNAs, estimate the timing of the transfers, and understand the molecular mechanisms involved.Ancestral and recent HGT events replaced and enlarged the multichromosomal mtDNA of Lophophytum spp., with the foreign DNA ascending to 74%. A total of 14 foreign mitochondrial chromosomes originated from continuous regions in the host mtDNA flanked by short direct repeats. These foreign tracts are circularized by microhomology‐mediated repair pathways and replicate independently until they are lost or they eventually recombine with other chromosomes. The foreign noncoding chromosomes are variably present in the population and likely evolve by genetic drift.We present the 'circle‐mediated HGT' model in which foreign mitochondrial DNA tracts become circular and are maintained as plasmid‐like molecules. This model challenges the conventional belief that foreign DNA must be integrated into the recipient genome for successful HGT. [ABSTRACT FROM AUTHOR]

Vietnam, a nation with a rich and complex history of migration and settlement, is home to 5 fundamental language families: Austroasiatic (AA), Tai-Kadai (TK), Austronesian (AN), Sino-Tibetan (ST) and Hmong-Mien (HM). Among them is the Austronesian, a language family substantial in island Southeast Asia (ISEA) but marginal in mainland counterpart (MSEA), constituted five Vietnamese ethnolinguistic groups. Here, we analyzed the control region, and the complete mitochondrial DNA (mtDNA) of 121 individuals from 3 AN-speaking populations (Churu, Ede, and Giarai). To explore the molecular diversity, the sequences were aligned against the Reconstructed Sapiens Reference Sequence (RSRS). The quantification and distribution of nucleotide variations resulted in 6,369 variants in our dataset in which the control region and coding region retained 1,707 and 4,662 variants, respectively. Churu harbored the most diversity (54.6 ± 2.8 variants/person), followed by Giarai (52.2 ± 3.3 variants/person), and Ede (51.1 ± 5.3 variants/person). Both the control region and whole mtDNA were input to Haplogrep3 to call haplogroups, resulting in 47.11% of our samples having their haplogroup changed from 17 whole mtDNA lineages to 16 different control region lineages. The haplogroup profile derived from whole mtDNA included 31 unique clades, in which only B5a1d was shared among three groups, and 23/31 lineages were present exclusively in a single population. The haplogroup component of each minority also revealed that all 3 AN groups had the majority of their samples attributed to the macrohaplogroups M, B, and F, with the disparity fixed in their underlying sublineages. This study increased the knowledge wealth of the genetic characteristics of AN speakers in the region from a different analysis approach, and highlighted the contribution of variants in different complete mtDNA, providing insight to reconstruct a comprehensive genetic architecture of Vietnam. [ABSTRACT FROM AUTHOR]

The wolf spider Pardosa astrigera L. Koch, 1878, an important biological control agent for pests in agriculture, is widely distributed in various ecosystems across East Asia. This study used mitochondrial DNA and aimed to provide an in-depth understanding of population genetic structure and evolutionary history throughout the species. Mitochondrial gene sequences from 107 samples of P. astrigera from 25 East Asian populations were used for genetic analyses. Our data revealed an asymmetric phylogeographic distribution in two sympatric lineages (1–2) of P. astrigera in continental East Asia. The spatio-temporal pattern of two mitotypes of P. astrigera in this region gives strong support for a Northeast Asian origin during the late Pleistocene (~1.69 million years ago) and the population expansion time of ~74,340 (58,832–104,236) years ago (during the last glacial period) and dual colonization around East Asia from two directions: from North to South and from East to West. Our phylogeographic results suggested that Pleistocene climate oscillations with subsequent fragmentation events and secondary contacts were the major impact factors of the diversification, geographic distribution, and expansion patterns of P. astrigera, and human activities and ballooning probably accelerated its recent dispersal. [ABSTRACT FROM AUTHOR]

Genetic relationships were examined for a total of 90 individuals of 90 species or species var. from 13 genera of Malawian cichlids based on the sequences of an amplified 991‐bp fragment of the mtDNA control region (mtDNA‐CR). In the network analysis, no exclusive clades were made by all the members of any genera in this study. However, congeneric clades were observed by genera Buccochromis, Copadichromis, Protomelas, and Sciaenochromis, whereas no congeneric clades were observed by genera Mylochromis, Nimbochromis, and Otopharynx. In non‐mbuna, an Aulonocara–Lethrinops group was divided into two groups, and the mean genetic distance of the larger group was much lower from mbuna than from other non‐mbuna. Overall mean genetic distance within a genus was generally low in mbuna, whereas it was relatively high in non‐mbuna. In the genetic tree of each genus, two or more large clades were observed, and some clades, such as those of Aulonocara hansbaenschi and Aulonocara nyassae in genus Aulonocara, Lethrinops micrentodon and Lethrinops sp. "gold harbor" in Lethrinops, and Otopharynx ovatus and Otopharynx brooksi in Otopharynx, were very deeply differentiated. Besides, a mbuna species, Pseudotropheus crabro, was extremely deeply differentiated from other members of this genus. These results suggest a widespread morphological convergence across the taxa in parallel with deep genetic differentiation in the long evolutionary story and some possibility of generation of the species of Aulonocara–Lethrinops group by hybridization of small non‐mbuna and mbuna species. Furthermore, taxonomical reexamination is necessary based on a strong support by genetic connection. [ABSTRACT FROM AUTHOR]

The contemporary diversity and distribution of species are shaped by their evolutionary and ecological history. This can be deciphered with the help of phylogenetic and demographic analysis methods, ideally combining and supplementing information from mitochondrial and nuclear genomes. In this study, we investigated the demographic history of Eurasian perch (Perca fluviatilis), a highly adaptable teleost with a distribution range across Eurasia. We combined whole‐genome resequencing data with available genomic resources to analyse the phylogeny, phylogeography, and demographic history of P. fluviatilis populations from Europe and Siberia. We identified five highly diverged evolutionary mtDNA lineages, three of which show a strong signal of admixture in the Baltic Sea region. The estimated mean divergence time between these lineages ranged from 0.24 to 1.42 million years. Based on nuclear genomes, two distinct demographic trajectories were observed in European and Siberian samples reflecting contrasting demographic histories ca. 30,000–100,000 years before the present. A comparison of mtDNA and nuclear DNA evolutionary trees and AMOVA revealed concordances, as well as incongruences, between the two types of data, most likely reflecting recent postglacial colonization and hybridization events. Overall, our findings demonstrate the power and usefulness of genome‐wide information for delineating historical processes that have shaped the genome of P. fluviatilis. We also highlight the added value of data‐mining existing transcriptomic resources to complement novel sequence data, helping to shed light on putative glacial refugia and postglacial recolonization routes. [ABSTRACT FROM AUTHOR]

This study confirms the extended distribution of two invasive species of the genus Ameiurus in Ukraine. Specifically, A. melas is recorded for the first time in the Southern Buh basin and A. nebulosus has expanded further eastward within the Dnipro basin. Material collected in 2019 and 2022 was identified by morphological features and confirmed by molecular genetic analysis. The most reliable morphological characters for distinguishing these two species include anal‐fin membrane pigmentation (light or black), gill raker count (fewer or more than 16), and serrations on the pectoral‐fin spine (well‐developed along the full length or small, absent near the tip). The analysis of the cytochrome oxidase subunit I barcoding marker identified all samples from the Dnipro Basin (Tnia and Velykyi Luh localities) as A. nebulosus, while all specimens from the Vinnytsia region within the Southern Buh basin (Sotskoho and Vyshenske lakes) were attributed to A. melas. The maximum‐likelihood analysis revealed clearly separated clades with high bootstrap support (>75%), strongly supporting the presence of the two separate species. This study suggests the potential for further eastward expansion of both species within Ukraine: A. nebulosus in the northern direction and A. melas in the southern direction. [ABSTRACT FROM AUTHOR]

Tenualosa ilisha is an anadromous fish from the Clupidae family that is distributed in several Asian countries. The relationship between T. ilisha from Indonesian waters and other waters in Asia is unknown, therefore this study was conducted to provide an overview of the relationship between T. ilisha from Indonesia and other waters in Asia based on the Cytochrome b gene (Cyt b) of mitochondrial DNA (mtDNA). The base sequence of T. ilisha from Labuhanbatu with a length of 568-572 base pairs (bp) was analyzed, then compared with Genbank data. All sequences compared showed that the composition of A+T (52.5%) was greater than G+C (47.5%). Genetic distance was calculated using Kimura two parameter (K2P); the lowest genetic distance of 0.000 was obtained between T. ilisha Labuhanbatu and Iraq with accession numbers LC619671.1; LC619673.1; LC619674.1. Meanwhile, the highest genetic distance is known to be 0.021 between T. ilisha Labuhanbatu and Bangladesh with the accession numbers MN748964.1, and MN748966.1. Neighbor-joining and maximum likelihood with 1000x repetition were the phylogenetic methods used to analyze the evolutionary relationships of T. ilisha. In general, both methods showed the same result that T. ilisha from Indonesia and other Asian waters are the same population. [ABSTRACT FROM AUTHOR]

The house mouse is the best-studied mammal species after humans, yet our understanding of its evolutionary history remains incomplete. Here, we focused on the colonisation of Europe by two subspecies and formation of a hybrid zone between them. We carried out a large-scale study of ~7000 mice sampled across an area embracing an ~900 km long portion of the zone, supplemented with cytochrome b and D-loop sequencing of ~1200 individuals collected worldwide. We demonstrate that the course of the mtDNA contact front is intricate and highly discordant with the consensus front for autosomal and X-linked markers, suggesting that local snapshots of mtDNA introgression may be misleading when treated in isolation. While multiple unrelated M. m. domesticus haplotypes occur in the zone area, the diversity of M. m. musculus haplotypes is limited. Moreover, we uncovered a vast region of domesticus introgression into musculus territory in northern areas and showed this introgression is unlikely to be driven by positive selection. We consider two previously published hypotheses explaining this phenomenon and put forth an alternative scenario assuming associations between mice and humans in northern Europe during the Nordic Bronze Age and subsequent zone movement associated with the expansion of Balto-Slavic peoples. [ABSTRACT FROM AUTHOR]

The Atlantic blue crab, Callinectes sapidus, is acknowledged as one of the worst invasive alien species in the Mediterranean, impacting biodiversity and human activities. Native to the western Atlantic, it has expanded to European coastal waters since the early 1900s. Despite its ecological and commercial importance, genetic research on this species is limited. Here we show a comprehensive investigation of the genetic variation and evolutionary history in Callinectes sapidus using 667 mitochondrial COI gene sequences. Our dataset encompasses 36 newly generated sequences from previously understudied Mediterranean sites and 631 from worldwide locations obtained from the GenBank public database. Our findings reveal two distinct, but closely related, genetic groups within the species' distribution range, suggesting the occurrence of a potential species complex. Furthermore, in the Mediterranean, low levels of genetic variability were observed except for substantial haplotypic differentiation in Turkish samples. This study depicts the global genetic diversity and evolutionary patterns of Callinectes sapidus, offering new insights into the taxonomic status of the species. [ABSTRACT FROM AUTHOR]

Simple Summary: The grey partridge (Perdix perdix Linnaeus, 1758), is a polytypic species with seven recognized subspecies, including one subspecies (P. p. italica Hartert, 1917) that is endemic to the Italian peninsula. Until World War II, the species was widespread across Europe, but then severely declined due to anthropogenic causes, including hybridization. The contraction of the endemic population distribution range and the introduction of allochthonous genotypes that started at the beginning of the past century led to the impoverishment of the endemic gene pool. This is still one of the main threats to this species and is only partially managed through ex situ conservation programs. To understand the native genetic composition of Italian grey partridge, we performed genetic characterization of museum specimens, proving that museum samples are a reliable source of DNA for investigating the genetic structure of species or populations from the recent past. The data obtained highlight, along with a contraction in the distribution, a high presence of specimens coming from other European populations, suggesting an uncertain situation of the species in Italy, despite the conservation efforts made. Extensive historical bibliographic research allowed us to define time baselines and periods with different restocking pressures. The grey partridge (Perdix perdix Linnaeus, 1758), is a polytypic species with seven recognized subspecies, including P. p. italica (Hartert, 1917), which is endemic to Italy. Until World War II, the species was widespread across Europe but severely declined due to anthropogenic causes, jeopardizing the Italian subspecies gene pool. Genetic characterization and haplotype identification were performed by analyzing the 5′-end of the mitochondrial control region (CR). A total of 15 haplotypes were detected, seven of which were present in the population before 1915. Among them, three haplotypes were never detected again in the individuals collected after 1915. Interestingly, eight of the 15 haplotypes detected in Italian museum samples belonged exclusively to individuals collected after 1915. The obtained data highlight a high presence of specimens originating from other European populations and, despite all the conservation efforts, suggest an uncertain situation of the subspecies in Italy. This research was strongly backed up by extensive bibliographic research on historical documents, allowing the identification of hundreds of restocking events all over Italy. This is an integral part of this research and has laid the foundations for identifying and circumscribing historical periods in which introductions from the rest of Europe had different pressures, aiming to define a baseline. [ABSTRACT FROM AUTHOR]

Sequencing the mitochondrial genome of the tunicate Oikopleura dioica is a challenging task due to the presence of long poly-A/T homopolymer stretches, which impair sequencing and assembly. Here, we report on the sequencing and annotation of the majority of the mitochondrial genome of O. dioica by means of combining several DNA and amplicon reads obtained by Illumina and MinIon Oxford Nanopore Technologies with public RNA sequences. We document extensive RNA editing, since all homopolymer stretches present in the mitochondrial DNA correspond to 6U-regions in the mitochondrial RNA. Out of the 13 canonical protein-coding genes, we were able to detect eight, plus an unassigned open reading frame that lacked sequence similarity to canonical mitochondrial protein-coding genes. We show that the nad3 gene has been transferred to the nucleus and acquired a mitochondria-targeting signal. In addition to two very short rRNAs, we could only identify a single tRNA (tRNA-Met), suggesting multiple losses of tRNA genes, supported by a corresponding loss of mitochondrial aminoacyl-tRNA synthetases in the nuclear genome. Based on the eight canonical protein-coding genes identified, we reconstructed maximum likelihood and Bayesian phylogenetic trees and inferred an extreme evolutionary rate of this mitochondrial genome. The phylogenetic position of appendicularians among tunicates, however, could not be accurately determined. [ABSTRACT FROM AUTHOR]

The genus Pseudamnicola Paulucci, 1878, is commonly found throughout the Mediterranean region. The genus displays considerable levels of endemism, accompanied by notable systematic and taxonomic ambiguity. However, the application of molecular data has proven highly effective in clarifying taxonomy and unveiling the diversity of cryptic species within the genus. Therefore, we employed all cytochrome c oxidase subunit I sequence data available and generated new ones from Greece to infer the phylogeny of the genus throughout its Mediterranean range and estimate the divergence times as well as the ancestral area of diversification. Our phylogenetic and time‐estimate analyses demonstrate that with 36 to 38 extant Pseudamnicola species and genetic divergences across species ranging from 0.5% to 11.9% on average, the genus underwent relatively recent diversification during late Miocene (6.53 Ma), and the primary speciation events occurred during Plio‐Pleistocene. The Italian Peninsula and Islands and the Ionian Drainages as defined by the Freshwater Ecoregions of the World are the ancestral regions of the genus following two different dispersal routes. Our study contributes to deepening our understanding of Pseudamnicola phylogeny by using data from throughout its range for the first time. This phylogeny provides evidence and confirms previous studies that relatively recent habitat isolation, followed by founder and dispersal events, has been one of the primary reasons for the evolution of the genus Pseudamnicola in the Mediterranean basin. [ABSTRACT FROM AUTHOR]

Biological invasions are among the major stressors on aquatic ecosystems. It can significantly affect species distribution and native biodiversity. Penaeus monodon invasions are frequently reported worldwide, leading to the establishment of several breeding populations. P. monodon was first recorded and morphologically identified in the Mediterranean Sea in Egypt in 2016. The current investigation aimed to assess the genetic diversity and origin of a P. monodon population from the Mediterranean Sea, Egypt, and to evaluate the genetic diversity of P. monodon populations worldwide using two different mitochondrial barcode regions, cytochrome c oxidase subunit I (COI) and 16S rRNA. Different P. monodon populations with Indo-Pacific and Atlantic origins were included for these purposes. Based on the COI, 16 haplotypes were recorded in nine P. monodon populations, with 45 polymorphic sites. High haplotype diversity (Hd = 0.7575) and high nucleotide diversity (π = 0.0261) were also recorded. Based on 16S rRNA, 37 haplotypes were recorded in seven P. monodon populations, with 72 polymorphic sites, high haplotype diversity (Hd = 0.9838), and high nucleotide diversity (π = 0.0985). The populations of P. monodon within its species range (of Indo-Pacific and Atlantic origins) shared many haplotypes, indicating shared lineages. Barrier analysis has divided the studied populations into groups in which Egypt was grouped with populations of Atlantic origin (based on COI and 16S rRNA) and supported with evidence of the Atlantic origin of the Egyptian population. This study showed that the Suez Canal is not the inevitable route for this species to invade the Mediterranean; therefore, precision must be exercised when determining the route of entry of any species into the Mediterranean Sea. The frequent introductions/invasions of the P. monodon population significantly contributed to the observed patterns of genetic diversity and favored its ability to adapt, colonize, and expand. [ABSTRACT FROM AUTHOR]

Massively parallel sequencing (MPS) technology has become the gold standard in mitochondrial DNA research due to its high sensitivity in detecting mtDNA heteroplasmy, a prognostic marker in various medical applications. Various MPS technologies and platforms used for mtDNA analysis exist. Obtaining reliable and sensitive results requires deep and uniform coverage of the entire mtDNA sequence, which is heavily influenced by the choice of library preparation method and sequencing platform. Here, we present a comparison of the sequencing coverage and the ability to heteroplasmy detection using two library preparation protocols (Nextera XT DNA Library Preparation Kit and Nextera DNA Flex Library Preparation Kit) and two different (MiSeq FGx and ISeq 100) Illumina MPS platforms. Our study indicates that the Nextera DNA Flex Library protocol provides a more balanced coverage along the mitogenome and a reliable heteroplasmy detection with both MiSeq and iSeq Illumina MPS systems. [ABSTRACT FROM AUTHOR]

Beryllium sulfate (BeSO4) can cause inflammation through the mechanism, which has not been elucidated. Mitochondrial DNA (mtDNA) is a key contributor of inflammation. With mitochondrial damage, released mtDNA can bind to specific receptors (e.g., cGAS) and then activate related pathway to promote inflammatory responses. To investigate the mechanism of mtDNA in BeSO4‐induced inflammatory response in 16HBE cells, we established the BeSO4‐induced 16HBE cell inflammation model and the ethidium bromide (EB)‐induced ρ016HBE cell model to detect the mtDNA content, oxidative stress‐related markers, mitochondrial membrane potential, the expression of the cGAS‐STING pathway, and inflammation‐related factors. Our results showed that BeSO4 caused oxidative stress, decline of mitochondrial membrane potential, and the release of mtDNA into the cytoplasm of 16HBE cells. In addition, BeSO4 induced inflammation in 16HBE cells by activating the cGAS‐STING pathway. Furthermore, mtDNA deletion inhibited the expression of cGAS‐STING pathway, IL‐10, TNF‐α, and IFN‐β. This study revealed a novel mechanism of BeSO4‐induced inflammation in 16HBE cells, which contributes to the understanding of the molecular mechanism of beryllium and its compounds‐induced toxicity. In this study, the inflammation and ρ0 cells model based on 16HBE cells was established to detect the mtDNA content, mitochondrial function‐related markers, the expression of the cGAS‐STING pathway, and inflammation. We found that BeSO4 caused oxidative stress, mitochondrial membrane potential decline, and the release of mtDNA into cytoplasm. The cGAS‐STING pathway was activated in inflamed 16HBE cells. mtDNA deletion inhibited the expression of cGAS‐STING pathway and inflammation. Our results contribute to the understanding of the molecular mechanism of BeSO4‐induced toxicity. [ABSTRACT FROM AUTHOR]

The crabeater seal (Lobodon carcinophaga) is the most common Antarctic seal; however, it remains understudied regarding genetic aspects. This research examined the genetic diversity and population dynamics of the Danco Coast population in the Antarctic Peninsula and compared it with the Western Antarctica population. Twenty novel haplotypes were identified, revealing a stable population phase and a brief expansion. The high genetic diversity aligns with those found in similar species and environments. Historical population dynamics correlate with Pleistocene climate shifts, shedding light on climate change's impact on Antarctic ecosystems. This study increases our understanding of Antarctic seal species, contributing to the region's guidelines to improve environmental conservation policies in the Antarctic sector. [ABSTRACT FROM AUTHOR]

Abstract 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.

The effect of T. aestivum L. chromosomes 1A and 1D on fertility of recombinant bread wheat allolines of the same origin carrying the cytoplasm of barley H. vulgare L. and different levels of cytonuclear compatibility was studied. Alloline L-56 included mainly fully sterile (FS) and partially sterile (PS) plants, alloline L-57 included partially fertile (PF) plants and line L-58 included fertile (F) ones. Analysis of morphobiological traits and pollen painting indicated complete or partial male sterility in plants of allolines L-56 and L-57. To differentiate genotypes with cytonuclear coadaptation and genotypes with cytonuclear incompatibility, PCR analysis of the 18S/5S mitochondrial (mt) repeat was performed. Heteroplasmy (simultaneous presence of barley and wheat mtDNA copies) was found in FS, PS, PF and some F plants, which was associated with a violation of cytonuclear compatibility. Wheattype homoplasmy (hm) was detected in the majority of the fertile plants, which was associated with cytonuclear coadaptation. The allolines used as maternal genotypes were crossed with wheat-rye substitution lines 1R(1A) and 1R(1D). In F1, all plants of PF×1R(1A) and PF×1R(1D) combinations were fertile, and in F2, a segregation close to 3 (fertile) : 1 (sterile) was observed. These results showed for the first time that chromosomes 1A and 1D carry one dominant Rf gene, which controls the restoration of male fertility of bread wheat carrying the cytoplasm of H. vulgare. All plants of F1 combinations FS×1R(1A), FS×1R(1D), PS×1R(1A), PS×1R(1D) were sterile, which indicates that a single dose of genes localized on wheat chromosomes 1A or 1D is not enough to restore male fertility in FS and PS plants. All plants of hybrid combinations F(hm)×1R(1A) and F(hm)×1R(1D) in both F1 and F2 were fertile, that is, fertility of allolines with cytonuclear coadaptation does not depend on wheat chromosomes 1A and 1D.

Abstract Whole genome sequences (WGS) of 185 North American Thoroughbred horses were compared to quantify the number and frequency of variants, diversity of mitotypes, and autosomal runs of homozygosity (ROH). Of the samples, 82 horses were born between 1965 and 1986 (Group 1); the remaining 103, selected to maximize pedigree diversity, were born between 2000 and 2020 (Group 2). Over 14.3 million autosomal variants were identified with 4.5–5.0 million found per horse. Mitochondrial sequences associated the North American Thoroughbreds with 9 of 17 clades previously identified among diverse breeds. Individual coefficients of inbreeding, estimated from ROH, averaged 0.266 (Group 1) and 0.283 (Group 2). When SNP arrays were simulated using subsets of WGS markers, the arrays over-estimated lengths of ROH. WGS-based estimates of inbreeding were highly correlated (r > 0.98) with SNP array-based estimates, but only moderately correlated (r = 0.40) with inbreeding based on 5-generation pedigrees. On average, Group 1 horses had more heterozygous variants (P

Objective To investigate the role and possible mechanisms of transactive response DNA binding protein 43 (TDP-43) in mediating neuronal injury induced by oxidative stress in mouse neuro-2a (N2a) cells and mouse pain sensitization. Methods ① To evaluate the optimal induction concentration, N2a cells were treated with different concentrations of H2O2, and the cells were divided into control group, 200, 400 and 800 μmol/L H2O2 groups. ②To assess the optimal induction duration, N2a cells were treated with 400 μmol/L H2O2, and the cells were divided into control group, and the cell groups treated for 6, 12 and 24 h, respectively. ③To validate the mitochondrial DNA (mtDNA) release pathway, cyclosporin A (CsA) was used to inhibit the mitochondrial permeability transition pore (mPTP), and the cells were divided into control group, 24 h H2O2 group and 24 h H2O2+CsA group. ④To validate TDP-43-mediated cellular damage, the cells were divided into control group, 24 h H2O2 group and 24 h H2O2+siTDP-43 group. ⑤ Cell viability was assessed using CCK-8 assay, while cell proliferation was determined using EdU assay. Western blot analysis was employed to examine the expression levels of TDP-43, neuronal nuclei (NeuN), cyclic GMP-AMP synthase (cGAS), and stimulator of interferon genes (STING). qPCR was utilized to measure the release of mtDNA. Immunostaining was conducted to observe intracellular expression of TDP-43, and Calcein AM staining was employed to evaluate mPTP opening status. ⑥To elucidate the role of TDP-43 in neuropathic pain (NP), 24 healthy SPF male C57BL/6J mice (6~8 weeks old, 25~30 g) were randomly divided into control group, chronic constriction injury (CCI) group, and CCI+siTDP-43 group. In 1 d before and 7, 14 and 21 d after surgery, intrathecal injections of siTDP-43 were administered. Mechanical and thermal pain thresholds of the mice were assessed using von Frey filaments and radiant heat, respectively, on 1 preoperatively and 1, 3, 5, 7, 14 and 21 d postoperatively. Immunofluorescence assay was conducted on 21 d postoperatively to examine the changes in TDP-43 and NeuN in the lumbar spinal dorsal horn (L5-L6). Results Oxidative stress induced a significant increase in TDP-43 protein level in N2a cells, prompted mtDNA release through mPTP, markedly up-regulated the expression of cGAS and STING, and consequently impacted the viability of N2a cells (P

Objective To investigate the effects of damaged nerve-derived mitochondrial DNA (mtDNA) on GRP75 protein expression, mitochondrial Ca2+ level and apoptosis in human glioblastoma cell line U-87MG (U87) cells, and its mechanism of inducing pain sensitization in mice. Methods Chronic constriction injury (CCI) of the sciatic nerve was used to establish a mouse model of neuropathic pain (NeP). A total of 20 male C57BL/6 mice (6~8 weeks old, weighing 20~30 g) were randomly divided into sham group, and CCI-7, -14 and CCI-21 d groups. Paw withdrawal mechanical threshold (PWMT) was measured, and the changes in mtDNA content in the spinal cord were detected with quantitative real-time PCR (qPCR). After mtDNA was extracted from human neuroblastoma cells (SH-SY5Y) treated with H2O2, U87 cells were treated with mtDNA at a dose of 0~1 ng/μL. CCK-8 assay was utilized to detect cell viability, and the appropriate concentration was selected according to the results. Then U87 cells were divided into: control group, mtDNA group, mtDNA+GRP75 inhibitor (MKT-077 1 μg/mL) group, mtDNA+calcium chelator (BAPTA-AM 10 μmol/L) group, and mtDNA+MKT-077+BAPTA-AM group. MKT-077 and BAPTA-AM were pre-treated in 2 h before mtDNA treatment, respectively. Western blotting was employed to assess the expression of glucose-regulated protein 75 (GRP75) protein, and endoplasmic reticulum-mitochondrial colocalization staining was conducted to observe the endoplasmic reticulum-mitochondrial junction. Calcium ion fluorescent probe was used to measure mitochondrial Ca2+ levels. The oxidative stress and function of mitochondria were evaluated by reactive oxygen species (ROS) and mitochondrial membrane potential. PI fluorescent labeling was employed to examine apoptotic rate of U87 cells. Results Compared with the sham group, the cytochrome C oxidase I (CO1) and nicotinamide adenine dinucleotide dehydrogenase 1 (ND1), which were utilized to measure mtDNA content in the spinal cord of mice in the CCI-21 group, were increased (1.01±0.20 vs 2.22±0.26, P

The Hoplias malabaricus group comprises seven described species, including seven karyomorphs for H. malabaricus. However, the relationship between morphological and chromosomal data within the group remains unresolved. Most studies on the Hoplias malabaricus group from the Iguazu River ecoregion have primarily focused on its upper and middle sections, while the lower Iguazu River remains unstudied. Therefore, in this study, we investigated a population of H. malabaricus from the Capanema's River (lower Iguazu River basin), Brazil, using cytogenetic techniques and DNA barcode. Through these analyses, we identified the karyomorphs A and D living in sympatry in the lower Iguazu River basin. The karyomorph A, identified as native to the Iguazu River basin, had two cytotypes, designated as A1 and A2, which are differentiated by C-positive heterochromatin and rDNA distribution patterns. Conversely, this is the first record of karyomorph D for the Iguazu River basin, which was previously thought to be endemic to the Upper Paraná River basin and may therefore represent an introduced karyomorph. Interestingly, the cytotype A2 is very similar (same haplogroup) to sequences of Hoplias argentinensis, while the karyomorph D from the lower Iguazu River basin is similar to sequences identified as Hoplias misionera. These findings provided new insights into the diversity of Hoplias gr. malabaricus from the Neotropical region, achieved through cytogenetic and DNA barcode integration. The results also highlight the increased conservation risk for native species in the Iguazu River ecoregion, particularly considering the ecological position occupied by trahiras within the trophic levels. [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]

Knowledge of genetic variability within and among types and breeds of dromedary (Camelus dromedarius L.) can be a valuable asset in selective breeding of desirable characteristics and will shed light on their origin, dynamics of domestication, and dispersion. Variability in an 809 bp segment of the mtDNA genome was measured within and among dromedaries from eight indigenous and one exogenous breed from Ha'il in north-central Saudi Arabia. Sixteen mtDNA haplotypes were identified among 47 camels. Haplotypic diversity among breeds is high (Hd = 0.817); most of the AMOVA variance (55.05%) occurs within breeds. Phylogenetic comparison of these haplotypes with those obtained across their geographic range showed that most haplotypes were placed within the same cluster with ancient wild dromedaries and the two newly identified haplotypes in this study. The most prevalent haplotypes found in dromedaries from this area appear to be ancestral to most other dromedaries and differ from each other by only one SNP. These results support the hypothesis that the Arabian Peninsula is a hub of diversification for dromedaries. [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]

Graphical Abstract Research Highlight • The genetic diversity of Stiphodon semoni is high. • All populations have high haplotype diversity except for Cimaja. • No genetic structure is observed within the populations of semoni. • The population of semoni has undergone demographic expansion. • Cibareno River has the potential to be a protected area. Abstract Fishing activities negatively impact fish populations, potentially causing a decline in fish stocks. Nevertheless, ensuring diversity and connectivity among populations can mitigate these adverse effects. To evaluate the connectivity of river mouths in the western part of Southern Java waters, we sequenced forty Stiphodon semoni individuals from five populations using mitochondrial cytochrome oxidase subunit 1 as molecular markers. The study revealed that S. semoni populations showed high diversity (0.821), with the population in Cimaja displaying the lowest diversity (0.464). Furthermore, the result of the analysis of molecular variance was a Fst value of 0.0630 with a p-value of 0.22. These results along with the result of the haplotype network indicated no significant genetic differences among these populations. This implies that the river mouths in the western part of Southern Java waters are interconnected. The distribution of mismatches showed a single peak, indicating that the populations have undergone demographic expansion. This information could be valuable for the conservation and management of S. semoni in the western part of the Southern Java waters.

Abstract Background Liver surgery during the perioperative period often leads to a significant complication known as hepatic ischemia-reperfusion (I/R) injury. Hepatic I/R injury is linked to the innate immune response. The cGAS-STING pathway triggers the activation of innate immune through the detection of DNA within cells. Nevertheless, the precise mechanism and significance of the cGAS-STING pathway in hepatic I/R injury are yet to be investigated. Methods Mouse model of hepatic I/R injury was used in the C57BL/6 WT mice and the STING knockout (STING-KO) mice. In addition, purified primary hepatocytes were used to construct oxygen-glucose deprivation reperfusion (OGD-Rep) treatment models. Results Our research revealed a notable increase in mRNA and protein levels of cGAS and STING in liver during I/R injury. Interestingly, the lack of STING exhibited a safeguarding impact on hepatic I/R injury by suppressing the elevation of liver enzymes, liver cell death, and inflammation. Furthermore, pharmacological cGAS and STING inhibition recapitulated these phenomena. Macrophages play a crucial role in the activation of the cGAS-STING pathway during hepatic I/R injury. The cGAS-STING pathway experiences a significant decrease in activity and hepatic I/R injury is greatly diminished following the elimination of macrophages. Significantly, we demonstrate that the activation of the cGAS-STING pathway is primarily caused by the liberation of mitochondrial DNA (mtDNA) rather than nuclear DNA (nDNA). Moreover, the safeguarding of the liver against I/R injury is also attributed to the hindrance of mtDNA release through the utilization of inhibitors targeting mPTP and VDAC oligomerization. Conclusions The results of our study suggest that the release of mtDNA plays a significant role in causing damage to liver by activating the cGAS-STING pathway during I/R injury. Furthermore, inhibiting the release of mtDNA can provide effective protection against hepatic I/R injury.

Abstract Population-based studies of human mitochondrial genetic diversity often require the classification of mitochondrial DNA (mtDNA) haplotypes into more than 5400 described haplogroups, and further grouping those into hierarchically higher haplogroups. Such secondary haplogroup groupings (e.g., “macro-haplogroups”) vary across studies, as they depend on the sample quality, technical factors of haplogroup calling, the aims of the study, and the researchers' understanding of the mtDNA haplogroup nomenclature. Retention of historical nomenclature coupled with a growing number of newly described mtDNA lineages results in increasingly complex and inconsistent nomenclature that does not reflect phylogeny well. This “clutter” leaves room for grouping errors and inconsistencies across scientific publications, especially when the haplogroup names are used as a proxy for secondary groupings, and represents a source for scientific misinterpretation. Here we explore the effects of phylogenetically insensitive secondary mtDNA haplogroup groupings, and the lack of standardized secondary haplogroup groupings on downstream analyses and interpretation of genetic data. We demonstrate that frequency-based analyses produce inconsistent results when different secondary mtDNA groupings are applied, and thus allow for vastly different interpretations of the same genetic data. The lack of guidelines and recommendations on how to choose appropriate secondary haplogroup groupings presents an issue for the interpretation of results, as well as their comparison and reproducibility across studies. To reduce biases originating from arbitrarily defined secondary nomenclature-based groupings, we suggest that future updates of mtDNA phylogenies aimed for the use in mtDNA haplogroup nomenclature should also provide well-defined and standardized sets of phylogenetically meaningful algorithm-based secondary haplogroup groupings such as “macro-haplogroups”, “meso-haplogroups”, and “micro-haplogroups”. Ideally, each of the secondary haplogroup grouping levels should be informative about different human population history events. Those phylogenetically informative levels of haplogroup groupings can be easily defined using TreeCluster, and then implemented into haplogroup callers such as HaploGrep3. This would foster reproducibility across studies, provide a grouping standard for population-based studies, and reduce errors associated with haplogroup nomenclatures in future studies.

Abstract Background Understanding how endangered species respond to climatic changes is fundamental for their conservation. Due to its restricted geographic range, its sensitivity to the ongoing global warming and its continuing decline, the Southwestern-Alpine endemic wolf spider Vesubia jugorum is currently classified as Endangered in the IUCN Red List. Here, we combined species distribution modelling (SDM) and phylogeographic inference to describe the present, the past and the future of this species in light of the mtDNA genetic structure of extant populations. Results Phylogenetic and network analyses show a high level of genetic differentiation and a strong genetic structure of the populations, likely explicable by a long history of isolation and survival in separate refugia. The SDM projection into past climatic conditions supports these results by showing a smaller distribution range compared to present, mostly restricted to the Maritime and Ligurian Alps, which possibly served as main refugium. Future forecast shows a significant shift in the bioclimatic range towards higher altitudes and latitudes, with a drastic decrease of habitat suitability in the central and south-eastern parts of the range, with consequent general loss of haplotype diversity. Conclusion SDM and phylogeographic inference support the hypothesis that the current distribution and the genetic structure of the extant populations mirror the survival in situ of Vesubia jugorum across repeated glacial and interglacial phases, in line with the ‘long-term stability hypothesis’. Future predictions show a significant shift in the bioclimatic range that V. jugorum will be likely unable to track, with profound impact on its long-term survival and its genetic diversity. Our considerations have implication for conservation genetics, highlighting the pivotal role of the transboundary protected areas of the SW-Alps in promoting conservation efforts for this species.

Abstract Background Z-DNA binding protein 1 (ZBP1) is a nucleic acid sensor that is involved in multiple inflammatory diseases, but whether and how it contributes to osteoarthritis (OA) are unclear. Methods Cartilage tissues were harvested from patients with OA and a murine model of OA to evaluate ZBP1 expression. Subsequently, the functional role and mechanism of ZBP1 were examined in primary chondrocytes, and the role of ZBP1 in OA was explored in mouse models. Results We showed the upregulation of ZBP1 in articular cartilage originating from OA patients and mice with OA after destabilization of the medial meniscus (DMM) surgery. Specifically, knockdown of ZBP1 alleviated chondrocyte damage and protected mice from DMM-induced OA. Mechanistically, tumor necrosis factor alpha induced ZBP1 overexpression in an interferon regulatory factor 1 (IRF1)-dependent manner and elicited the activation of ZBP1 via mitochondrial DNA (mtDNA) release and ZBP1 binding. The upregulated and activated ZBP1 could interact with receptor-interacting protein kinase 1 and activate the transforming growth factor-beta-activated kinase 1-NF-κB signaling pathway, which led to chondrocyte inflammation and extracellular matrix degradation. Moreover, inhibition of the mtDNA-IRF1-ZBP1 axis with Cyclosporine A, a blocker of mtDNA release, could delay the progression of DMM-induced OA. Conclusions Our data revealed the pathological role of the mtDNA-IRF1-ZBP1 axis in OA chondrocytes, suggesting that inhibition of this axis could be a viable therapeutic approach for OA.

Abstract Background Cyperus stoloniferus is an important species in coastal ecosystems and possesses economic and ecological value. To elucidate the structural characteristics, variation, and evolution of the organelle genome of C. stoloniferus, we sequenced, assembled, and compared its mitochondrial and chloroplast genomes. Results We assembled the mitochondrial and chloroplast genomes of C. stoloniferus. The total length of the mitochondrial genome (mtDNA) was 927,413 bp, with a GC content of 40.59%. It consists of two circular DNAs, including 37 protein-coding genes (PCGs), 22 tRNAs, and five rRNAs. The length of the chloroplast genome (cpDNA) was 186,204 bp, containing 93 PCGs, 40 tRNAs, and 8 rRNAs. The mtDNA and cpDNA contained 81 and 129 tandem repeats, respectively, and 346 and 1,170 dispersed repeats, respectively, both of which have 270 simple sequence repeats. The third high-frequency codon (RSCU > 1) in the organellar genome tended to end at A or U, whereas the low-frequency codon (RSCU 1; in particular, atp9, atp6, and rps7 may have undergone potential positive selection. Conclusion We assembled and validated the mtDNA of C. stoloniferus, which contains a 15,034 bp reverse complementary sequence. The organelle genome sequence of C. stoloniferus provides valuable genomic resources for species identification, evolution, and comparative genomic research in Cyperaceae.

We examined the genetic diversity and connectivity of two indigenous Mediterranean goatfish species (Mullus barbatus and M. surmuletus), and a Lessepsian migrant species (Upeneus moluccensis), across the Nile Delta outflow using two mitochondrial DNA markers (COI and cyt b). Genetic diversity was high for the two Mediterranean species but relatively lower for the migrant species, suggesting founder effects after invasion from the Red Sea. Confirmation of this hypothesis, however, would require comparison with populations of origin in the Red Sea and the broader Indo-West Pacific. AMOVA and network analyses revealed no genetic partitioning for all species, indicating that the Nile outflow does not currently, and may not have historically, posed a significant barrier to larval dispersal in these goatfish, despite a present-day temperature and salinity gradient along the Mediterranean coastline of Egypt.

Abstract Bivalves are an extraordinary class of animals in which species with a doubly uniparental inheritance (DUI) of mitochondrial DNA have been described. DUI is characterized as a mitochondrial homoplasmy of females and heteroplasmy of male individuals where F-type mitogenomes are passed to the progeny with mother egg cells and divergent M-type mitogenomes are inherited with fathers sperm cells. However, in most cases only male individuals retain divergent mitogenome inherited with spermatozoa. Additionally, in many of bivalves, unique mitochondrial features, like additional genes, gene duplication, gene extensions, mitochondrial introns, and recombination, were observed. In this study, we sequenced and assembled male-type mitogenomes of three Donax species. Comparative analysis of mitochondrial sequences revealed a lack of all seven NADH dehydrogenase subunits as well as the presence of three long additional open reading frames lacking identifiable homology to any of the existing genes.