Search Results (179)

French Bulldogs, like other brachycephalic breeds, are predisposed to a variety of genetic and tumour-related disorders. While mitochondrial DNA (mtDNA) mutations have been documented in canine tumours, no prior study has examined the entire mitochondrial genome in this breed. In this study, we analysed mtDNA obtained from blood and tumour tissue of a 10-year-old male French Bulldog diagnosed with carcinoma planoepitheliale keratodes (G1). Complete sequencing and comparative bioinformatic analysis revealed 22 sequence variants, including nine in protein-coding genes, two in RNA-coding genes, two in the control region, and nine within the variable number tandem repeat (VNTR) region. Identical variants were present in both blood and tumour tissue, indicating that no detectable tumour-specific mtDNA mutations were observed. Notably, the m.1397A>T transversion in the 16S rRNA gene and an insertion (m.2679_2680insG) in the tRNA-Leu(UUR) gene were identified, both mapping to conserved loci in the human mitochondrial genome. Among the coding variants, four nonsynonymous variants (including p.Cys55Tyr and p.Ser471Asn) were detected, two of which affected highly conserved amino acid positions. Most nonsynonymous changes were localised in random coil regions and internal mitochondrial compartments, whereas synonymous changes appeared mainly within transmembrane helices. The control region displayed the highest degree of polymorphism, including eight positions with A/G heteroplasmy and one length variant due to polyT extension. These findings represent the first documentation of full mitochondrial genome sequence variants in a French Bulldog with cancer providing descriptive data for future breed population and oncological research. Further studies are warranted to determine whether these alterations are breed- or tumour-specific. Full article

Lepidochelys olivacea is the most abundant sea turtle species worldwide and exhibits a circumtropical distribution across the Atlantic, Pacific, and Indian Oceans. Global phylogeographic studies have identified three major mitochondrial lineages, but comparisons among regions remain limited by inconsistent mtDNA control-region fragment lengths, incompatible haplotype nomenclatures, and uneven geographic sampling. The East Pacific Regional Management Unit (RMU), which includes major nesting populations in Mexico and Costa Rica, experienced severe demographic declines during the twentieth century, and the effects of expanded sampling on current phylogeographic patterns remain uncertain. This study analyzed 1264 mtDNA control region sequences (474-bp and 653-bp fragments) to update and standardize the global genetic dataset of L. olivacea, incorporating novel samples from previously unsampled East Pacific localities. Clear phylogeographic differentiation among RMUs was detected and remained consistent across both sequence lengths, supporting the Atlantic (ATL), East Pacific (EP), and Indo-West Pacific (IWP) lineages. Shared haplotypes between the EP and IWP lineages likely reflect historical connectivity rather than contemporary transoceanic movements. The 653-bp dataset revealed greater haplotype diversity (78 haplotypes) than the 474-bp dataset (62 haplotypes), highlighting the improved resolution provided by the longer marker. Regional diversity patterns appeared to be influenced by sampling effort, particularly in underrepresented regions such as the West Indian Ocean. Negative neutrality indices in both Pacific RMUs suggested recent population expansion. This study establishes a standardized haplotype nomenclature for L. olivacea, provides an updated view of mitochondrial lineage distributions, and offers a robust framework for future phylogeographic and conservation studies across the species’ range. Full article

Background: The Chungtien schizothoracin (Ptychobarbus chungtienensis) is a threatened freshwater fish endemic to the Qinghai–Tibet Plateau and adjacent high-altitude regions of northwestern Yunnan, China. Although a complete mitochondrial genome of P. chungtienensis has been previously reported, direct comparison with a mitogenome generated using high-accuracy long-read sequencing can provide additional information on mitochondrial genome structure and sequence variation. This study aimed to assemble and annotate a complete mitogenome of P. chungtienensis using PacBio HiFi sequencing and to compare its mitogenomic characteristics with previously published Ptychobarbus mitogenomes. Methods: High-molecular-weight genomic DNA from a single specimen was sequenced using PacBio HiFi long-read technology. The mitochondrial genome was assembled using MitoHiFi, annotated using MitoFinder followed by manual curation, and compared with previously published Ptychobarbus mitogenomes. Phylogenetic relationships were evaluated using maximum-likelihood analysis with expanded taxon sampling, and selection pressure on the 13 mitochondrial protein-coding genes was assessed using dN/dS-based branch and branch-site models. Results: The assembled mitogenome is 16,583 bp in length and contains the typical 37 mitochondrial genes, including 13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes, together with a control region and the origin of light-strand replication (O_L). The overall A + T content was 54.97%. Direct comparison with the previously reported 16,970 bp mitogenome showed that the 387 bp length difference was concentrated in non-coding regions, particularly the control region and the tRNA-Thr–tRNA-Pro intergenic region. Phylogenetic analysis based on 22 complete mitogenomes placed the newly assembled P. chungtienensis sequence in a strongly supported mitochondrial clade with Schizothorax macropogon (bootstrap = 100%), whereas the previously reported P. chungtienensis sequence clustered with P. kaznakovi (bootstrap = 100%), indicating that the two P. chungtienensis records represent distinct mitochondrial lineages. The dN/dS values of all 13 mitochondrial protein-coding genes were below 1, and neither branch nor branch–site analyses detected significant evidence of lineage-specific positive selection. Conclusions: This long-read-based mitogenome provides a high-quality genomic resource for P. chungtienensis and reveals substantial mitochondrial sequence and lineage variation among available records. These results provide a basis for comparative mitogenomic and conservation genetic studies while also indicating that species-level phylogenetic relationships and high-altitude adaptation should not be inferred from mitochondrial data alone. Full article

Turkmen populations remain underrepresented in genome-wide reference datasets, limiting comparative analyses of genetic diversity in Central Asia. This study provides an initial regional genome-wide characterization of self-identified Turkmen students who were studying in Kazakhstan at the time of sample collection and who reported the Dashoguz Region, Turkmenistan, as their place of birth in the questionnaire. Approximately 650,000 markers were genotyped in 25 participants, of whom 23 unrelated individuals were retained after genotype quality control and relatedness filtering. Population structure was evaluated with 600 present-day Eurasian reference individuals using principal component analysis, ADMIXTURE v1.3.0, and pairwise Weir–Cockerham F_ST estimates based on 17,471 linkage-disequilibrium-pruned autosomal SNPs. Runs of homozygosity, Y-chromosome haplogroups, and mitochondrial DNA haplogroups were also examined. The analyzed cohort was positioned within the Central Asian genetic landscape and showed the lowest pairwise differentiation from Uzbek, Tajik, and AADR Turkmen reference groups. Runs-of-homozygosity analysis showed mostly low-to-moderate individual burdens, although one individual had elevated long-segment homozygosity; sensitivity analyses indicated that the main autosomal results were not driven by this individual. Paternal and maternal haplogroup assignments revealed diverse uniparental lineages. These data provide a regional genome-wide resource for future comparative studies of Central Asian genetic diversity and have been deposited in the European Variation Archive. Full article

Introduction: Brown trout (Salmo trutta L.) is a salmonid fish considered a genetically and geographically highly structured species. The species is catalogued as vulnerable in the Spanish Red List since 1992. Based on morphological differentiation, some authors have proposed splitting Salmo trutta into many taxa and in recent years, several binomials involving morphologically differentiated Western Mediterranean brown trout morphs have regained relevance as distinct species and are now assessed in the IUCN Red List. However, Spanish legislation still considers a single species, S. trutta, inhabiting Atlantic and Mediterranean rivers. Analyses of mitochondrial DNA variation across the species’ native range have revealed numerous matrilineal lineages and helped disentangle the phylogenetic relationships and biogeographic history of brown trout. Four largely distant evolutionary lineages defined by sequencing the mitochondrial control region (Adriatic, AD, Mediterranean, ME, Atlantic, AT and Duero, DU) are native among the Iberian brown trout populations. Stocking activities have resulted in introgressive hybridization of these native populations with non-native northern Atlantic stocks throughout the Iberian rivers and compromise the evolutionary singularities of brown trout in the Iberian Peninsula. Methodology: In this study, we compare complete mitogenomes from Iberian brown trout specimens with those from other regions, using both newly sequenced samples and whole mitogenomes from the GenBank database and estimate their divergence times relative to those observed among species of other Salmoninae genera, such as Oncorhynchus and Salvelinus, to assess patterns of species-specific divergence among Iberian brown trout populations. Results: The evolutionary relationships of the specimens using their mitogenomes fitted with previous analyses using partial mitochondrial sequences and confirmed the strong differentiation among the Iberian lineages. All the branches involving distant Iberian mitogenomes are sister branches with taxa historically described under different binomials (such as Salmo macrostigma, S. multipunctatus, S. pallaryi). Conclusions: The results provide evidence supporting the existence of potentially distinct and undescribed native Salmo species in the Iberian rivers. Full article

Introduction: The Catalan chub (Squalius laietanus) is a freshwater cyprinid endemic to Catalonia, from the lower course of the Ebro River to the Tech, Tet, Agly, and Massane rivers in France. Classified as Vulnerable in the IUCN Red List (2024), its populations face significant threats due to anthropogenic pressures and the potential hybridization with the European chub (Squalius cephalus). Objective: This study aimed to characterize the genetic variation of the mitochondrial control region (CR) of S. laietanus across the main Catalan river basins to determine the population genetic structure of this species in the core of its distribution range. Methodology: A 789 bp fragment of the CR was sequenced in 334 chubs from 24 sampling sites collected by electrofishing between 2021 and 2025. The S. laietanus specific matrilineage of all these specimens had been previously detected by sequencing the Cytochrome c oxidase subunit I (COI) but this marker did not detect clear genetic structuring among basins. Results: In contrast to the low diversity within and among locations reported by COI, the CR showed a population structure distinguishing between northern (Muga, Fluvià, Daró, Ter, and Tordera rivers) and southern basins (Besòs, Llobregat, Gaià, Francolí, and Ebro rivers). In the southern rivers, a single haplotype, (H1), was present. This haplotype declined in abundance towards the north, being replaced with H2. In the Muga River, native Catalan chub populations showed the fixed H3 haplotype, suggesting strong isolation, while populations from the Daró River contained a private haplotype (H4). In contrast, the presence of a common and single haplotype in southern basins possibly resulted from genetic drift under strong summer droughts. Conclusions: Overall, these results reveal population structuring in S. laietanus and highlight the importance of considering regional differentiation in conservation and management strategies. Full article

Helminth infections remain a major constraint to livestock productivity, particularly in regions where domestic animals and wildlife share grazing habitats. This study investigated the molecular diversity and transmission dynamics of helminth communities in sheep (Ovis aries) and saiga antelope (Saiga tatarica) in West Kazakhstan. A total of 35 animals (20 sheep and 15 saiga) were examined, and helminths were identified using polymerase chain reaction targeting the ITS1 region of ribosomal DNA for nematodes and the mitochondrial cox1 gene for cestodes. Of the 20 analyzed samples, 80% were successfully identified at the molecular level. Detected species included Haemonchus contortus, Trichuris ovis, Chabertia ovina, Moniezia expansa, and Avitellina centripunctata. Phylogenetic analysis revealed that Chabertia ovina isolates from both hosts clustered within a single monophyletic clade, indicating high genetic similarity and supporting potential cross-species transmission. Mitochondrial markers provided higher resolution for cestode differentiation, whereas ITS1 was effective for nematode identification. The predominance of Chabertia ovina in saiga suggests ecological adaptation and efficient transmission within wild populations. These findings highlight the epidemiological significance of shared grazing ecosystems and underscore the need for integrated parasite control strategies that consider both livestock and wildlife reservoirs. Full article

Environmental DNA (eDNA) metabarcoding has emerged as a powerful tool for biodiversity monitoring, yet its accuracy is fundamentally constrained by the completeness and taxonomic reliability of reference sequence databases. For the Three Gorges Reservoir (TGR), no integrated multi-marker eDNA reference library exists, hampering standardized fish conservation monitoring under the Yangtze River Ten-Year Fishing Ban. Here, we constructed a comprehensive, multi-marker eDNA reference database for the fish fauna of the TGR, encompassing mitochondrial 12S rRNA, 16S rRNA, and cytochrome c oxidase subunit I (COI) gene sequences from 173 specimens (120 species) collected between 2021 and 2024. After integrating publicly available sequences, the final database comprised 161 species. Then, we quantitatively compared species annotation performance between this local database and public repositories. Results showed that while public databases achieved higher nominal species coverage (94.67%), they exhibited critical deficiencies in annotation accuracy, correctly annotating only 77.97% (12S rRNA), 75.00% (16S rRNA), and 38.14% (COI) of sequences from shared species under controlled conditions. In contrast, the local database exhibited 92.37%, 93.10% and 100% annotation accuracy for the respective markers. Optimal interspecific Kimura 2-parameter (K2P) thresholds for species delimitation were 0.00448 (12S rRNA), 0.00531 (16S rRNA), and 0.00734 (COI). In addition, 15, 0, and 4 species pairs exhibited zero interspecific distance for 12S rRNA, 16S rRNA, and COI, respectively. These limitations reinforce the need for cautious interpretation of eDNA metabarcoding results and the integration of multiple markers or complementary nuclear loci. This study provides preliminary evidence that regionally curated, multi-marker reference libraries could improve taxonomic assignment reliability in eDNA metabarcoding compared to uncurated public repositories, providing a foundational resource for biodiversity conservation. Full article

Background: Pangolins are critically endangered mammals, and a comprehensive understanding of their genetic diversity is crucial for effective conservation. The mitochondrial genome serves as a vital molecular marker for phylogenetic and population genetic studies. Obtaining genetic material from these elusive animals non-invasively remains a challenge. This study aimed to sequence and characterize the complete mitochondrial genome of Manis javanica and explore the phylogenetic relationships among pangolin species. Methods: The complete mitochondrial genome was sequenced from a saliva-derived sample. Standard procedures for DNA extraction, amplification, and sequencing were employed. The genome was assembled and annotated using bioinformatic tools. Phylogenetic analysis was conducted based on the cytochrome c oxidase subunit I (COXI) gene sequences from nine pangolin species, with the resulting tree constructed using the maximum-likelihood method. Results: The complete mitochondrial genome of M. javanica (GenBank accession: PP110760) is a circular molecule of 16,573 bp, containing 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a control region. The overall base composition showed a lower GC content (43.83%) than AT content (56.17%). Phylogenetic analysis based on COXI sequences delineated the nine species into three distinct genera: Manis, Phataginus, and Smutsia. Within the genus Manis, Manis pentadactyla was identified as the closest relative to M. javanica. The newly described species Manis mysteria was found to be closer to Manis culionensis and Manis crassicaudata than to other congeners. Furthermore, the analysis indicated that African pangolins diverged earlier than Asian pangolins. Conclusions: This study successfully demonstrates the feasibility of extracting and sequencing the complete mitochondrial genome from saliva samples, providing a valuable non-invasive method for future genetic studies on pangolins. The genomic data and phylogenetic results offer significant molecular insights that will benefit the genetic management and conservation of critically endangered pangolin resources. Full article

Populations of several billfish species are declining due to overfishing and bycatch, and fundamental aspects of their biology and population dynamics remain poorly understood. We provide the first assessment of the population genetic structure of longbill spearfish (Tetrapturus pfluegeri) in the western Atlantic Ocean. We screened variation at 12 nuclear microsatellite loci (n = 144) and mitochondrial DNA control region sequences (mtCR, n = 177). Both marker types revealed three genetically differentiated clusters, with mean values for microsatellites showing differentiation of F_ST = 0.136 and D_EST = 0.201, and for mtCR F_ST = 0.645. Microsatellite markers demonstrated moderate-to-high genetic diversity, with a mean allelic richness of 6.73 alleles per locus, moderate heterozygosities (Ho = 0.446, He = 0.604), and a positive inbreeding coefficient (F_IS = 0.22) across the three sample collection sites. The overall estimated effective population size was 789.2 (95% CI: 246.7–∞). The mtCR exhibited 96 haplotypes, with high haplotype (0.989 ± 0.003) and nucleotide (0.025 ± 1.3%) diversities. We found higher mean relatedness within clusters than among them, supporting the interpretation of population subdivision and the Wahlund effect. Tajima’s D and Fu’s Fs were negative across all localities, with significant values observed along the Brazilian coast but not in the Caribbean Sea. These neutrality test results, together with low Harpending’s raggedness indices from DNA sequence mismatch distributions, are consistent with historical demographic expansion. Our findings establish a genetic baseline for fishery monitoring and management, contributing to the conservation of T. pfluegeri populations in the western Atlantic Ocean. Full article

Background: Wolfram syndrome (WFS) is a rare neurodegenerative disease that is genetically determined and inherited in an autosomal recessive manner. Although the first clinical symptom appearing in early childhood is diabetes mellitus, subsequent symptoms are associated with optic nerve atrophy, followed by central nervous system atrophy. Methods: The aim of the study was to analyse magnetic resonance images (MRI) of the brain in combination with single-voxel magnetic resonance spectroscopy (MRS) and to assess the copy number of mitochondrial DNA (mtDNA-CN) in 10 patients with WFS compared with a control group of 17 healthy individuals. Results: A significant decrease in the amount of selected metabolites was observed in WFS patients compared to controls in all assessed brain regions (pons, cerebellum, white matter, thalamus, and hippocampus). For three metabolites, Glutamate (Glu), Glutamate + Glutamine (Glx) and total N-acetylaspartate (TNAA), significant differences in concentrations were found between the study groups in almost all matrices evaluating specific areas of the brain (p < 0.011), with the exception of a trend toward reduced TNAA in the hippocampus (p = 0.065). In addition, patients with WFS had a significant decrease in the mitochondrial-to-nuclear DNA ratio compared to controls (p < 0.0003). Some metabolites, such as N-acetylaspartate and total N-acetylaspartate, showed strong correlations with specific regions of the visual pathway on MRI scans in patients with WFS. Conclusions: Selected brain metabolites and mtDNA-CN may become potential markers of WFS, and the results of this study may be used to define indicators for future therapeutic strategies. Full article

Postglacial expansion dynamics strongly influence the genetic structure of temperate species; however, mitochondrial data from the Baltic region are limited. To assess diversity, phylogenetic origins, and regional structuring, we analyzed mitochondrial cytochrome b (726 bp) and control region (421–422 bp) sequences of the common vole (Microtus arvalis Pallas, 1779) from Lithuania. Of the 91 cytb sequences and 70 control region sequences analyzed, five and four haplotypes were identified, respectively. Markedly low haplotype and nucleotide diversity compared with most European populations were detected. Phylogenetic Maximum Likelihood and network analyses revealed that all Lithuanian haplotypes belong to the eastern European lineage and are most closely related to Polish and central European samples, which supports recolonization from a Carpathian refugium. Despite the overall low variation, we detected two distinct mitochondrial groups: a highly differentiated western group and a second group encompassing eastern, northern, and central–southern populations. This strong regional structuring suggests limited maternal gene flow on a small geographic scale. There was no evidence of introgression from related taxa, such as Microtus obscurus. Our findings refine the phylogeographic context of Baltic M. arvalis and highlight the region’s role in shaping postglacial diversity patterns. Full article

Background/Objectives: Although the etiopathogenesis of autism spectrum disorder (ASD) remains incompletely elucidated, current evidence supports a multifactorial model involving genetic and environmental factors that interact to induce a heterogeneous range of symptoms. In recent years, epigenetic mechanisms, particularly DNA methylation, have been recognized as key contributors to ASD pathophysiology. Alterations in mitochondrial DNA (mtDNA) methylation are also emerging as relevant contributors in several human conditions. The mitochondrial D-loop, a non-coding control region essential for mtDNA replication and transcription, is considered a hotspot for epigenetic regulation and its methylation levels have been found altered in various diseases, such as cancer, metabolic disorders, and neurological illness. However, to date, no studies have investigated mtDNA methylation changes in ASD. Methods: We analyzed the average methylation levels of a fragment containing ten CpG sites within the D-loop region and the mtDNA copy number in peripheral blood samples from 49 children with ASD and 50 neurotypically developing (NT) controls using Methylation-Sensitive High-Resolution Melting and quantitative PCR. Results: No significant differences in D-loop methylation levels were observed between ASD and NT children. Similarly, the mtDNA copy number did not differ between the two groups. No significant correlations were found between D-loop methylation or mtDNA copy number and either ASD severity or age. Conclusions: This is the first study investigating mtDNA methylation in ASD. Our results indicate that methylation of the D-loop region and the mtDNA copy number are not altered in ASD children. Further studies including larger cohorts and extended mtDNA regions are warranted to confirm and expand these findings. Full article

Fascioliasis, a globally prevalent zoonosis, severely threatens public health and livestock security. Current diagnostic approaches, hindered by the need for sophisticated instrumentation and specialized expertise, are inadequate for on-site surveillance in resource-constrained settings. This study developed a rapid, visual detection assay for Fasciola hepatica via recombinase-aided amplification (RAA) integrated with CRISPR/Cas12b, addressing critical equipment and operational constraints. Targeting a specific mitochondrial DNA fragment of F. hepatica, recombinant plasmid standards were constructed, RAA primers and sgRNA optimized, and three detection modalities (real-time fluorescence, UV lamp, test strip) integrated. Clinical validation against PCR demonstrated 45 min turnaround time, F. hepatica-specific positivity, and real-time fluorescence sensitivity of 2.6 copies/μL. Results showed high concordance with PCR and qPCR, with substantially reduced assay duration and streamlined workflow. This highly sensitive, specific, multi-visualized method overcomes limitations of conventional techniques, offering an efficient, field-deployable tool for fascioliasis surveillance and control in grassroots and pastoral regions. Full article

The blackfin flounder (Glyptocephalus stelleri) is an important demersal fish species widely distributed in the Northwest Pacific and represents a valuable fisheries resource in Korea and Japan. Understanding the genetic diversity and population connectivity of exploited marine species is essential for effective fisheries management and conservation. In this study, mitochondrial DNA control region sequences (401 bp) were analyzed from 62 individuals collected from Jumunjin, Korea, and Maizuru, Japan, to assess genetic diversity, demographic history, and population structure. Sequence analysis identified 48 haplotypes, revealing exceptionally high haplotype diversity (h = 0.982 ± 0.010) and relatively low nucleotide diversity (π = 0.011 ± 0.006). Neutrality tests and mismatch distribution analyses indicated a historical demographic expansion during the Pleistocene. No significant genetic differentiation was detected between the two sampling locations (F_ST = −0.004, p > 0.05), suggesting strong genetic connectivity between Korean and Japanese samples based on mitochondrial DNA data. These findings provide important baseline genetic information for understanding population connectivity and may contribute to the coordinated management of blackfin flounder fisheries in the Northwest Pacific. Full article