Search Results (950)

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

Acanthopleura loochooana is a widely distributed intertidal chiton in the northwestern Pacific, yet its mitochondrial genomic architecture and evolutionary position within Chitonidae have not been comprehensively evaluated. In this study, we sequenced and analyzed the complete mitochondrial genome of A. loochooana using next-generation sequencing. The mitogenome is a circular double-stranded DNA molecule of 15,295 bp that contains the typical 37 mitochondrial genes, including 13 protein-coding genes (PCGs), 22 transfer RNA genes, and 2 ribosomal RNA genes. Codon usage patterns show a clear preference for A- or U-ending codons, consistent with trends observed in other polyplacophoran mitogenomes. Phylogenetic analyses based on concatenated sequences of the 13 mitochondrial PCGs under Bayesian frameworks recovered congruent topologies with strong nodal support. A. loochooana was placed in a well-supported clade with Liolophura japonica and A. vaillantii, providing a reference within Acanthopleurinae. These results provide the complete mitochondrial genome of A. loochooana and contribute new mitogenomic data to the currently limited dataset of Polyplacophora, offering additional insights into mitochondrial genome organization and phylogenetic relationships within Acanthopleurinae. Full article

This study aimed to assess the species diversity and genetic structure of Meretrix clams around Hainan Island using mitochondrial cytochrome c oxidase subunit I (COI) DNA barcoding. The genus Meretrix is a common and economically important group of bivalves in the intertidal zones of Hainan Island, widely distributed in estuarine and nearshore sandy habitats and playing a significant role in local fisheries and aquaculture. In recent years, studies on Meretrix in Hainan have mainly focused on morphological identification and species records from limited coastal areas; however, due to the high phenotypic plasticity of shell morphology and the relatively subtle differences among species, traditional morphology-based identification remains challenging. Meanwhile, molecular systematic investigations of Meretrix in Hainan are still limited, particularly systematic studies using DNA barcoding to assess species diversity and geographic distribution patterns. A total of 141 individuals were collected from ten intertidal sites. Four species were identified—M. lyrata, M. lamarckii, M. meretrix and M. petechialis—with interspecific genetic distances (17.6–22.7%) far exceeding intraspecific variation (0.3–0.9%). Phylogenetic analysis based on COI sequences clearly distinguished four Meretrix species from the waters around Hainan Island, with each species forming a well-supported monophyletic clade, supporting their status as independent evolutionary lineages. In addition, two markedly divergent genetic lineages were detected within M. petechialis, suggesting that this species may possess a relatively complex population structure, one of which is typically found in northern Chinese waters, suggesting possible human-mediated introduction. Species richness was higher on the eastern coast, potentially influenced by regional hydrodynamic conditions. This study provides baseline DNA barcode data for Meretrix species in Hainan and supports the need for integrative management of this economically important resource. Full article

Background/Objectives: Early embryonic arrest during the cleavage stage (days 2–4) accounts for a substantial proportion of developmental failure in in vitro fertilization. This phenomenon remains poorly understood at the molecular level, even in chromosomally normal embryos identified by preimplantation genetic testing. This review aims to redefine cleavage-stage arrest from a passive energy deficit to a checkpoint-regulated endpoint caused by inadequate coordination among metabolism, transcriptome integrity, and stress-response pathways. Methods: We integrate evidence from long-read transcriptomics, metabolomics, epigenetics, and immunobiology relevant to pre-blastocyst development. These data are assembled into a unifying mechanistic framework and a clinically oriented stratification model, together with candidate multimodal readouts for early classification. Results: We propose a three-axis model linking: (i) metabolic–epigenetic insufficiency, including defective histone lactylation and impaired alpha-ketoglutarate-dependent DNA demethylation; (ii) isoform-level abnormalities, including intron retention and retrotransposon activation within a hidden transcriptomic landscape better resolved by long-read sequencing; and (iii) stress-related immune signaling, in which NLRP7 links alternative splicing and DNA-damage-response dysfunction with mitochondrial stress and p53-associated arrest. Within this framework, we distinguish three molecular arrest states: an early transition failure marked by defective maternal-to-embryonic reprogramming and severe splicing disruption; a metabolically quiescent state that may retain a limited rescue window; and a later stress-associated state characterized by senescence-like features, oxidative stress, and broad transcriptomic and genomic instability. Conclusions: Early embryo arrest should no longer be viewed as a nonspecific developmental failure, but as a mechanistically stratifiable condition with distinct metabolic, transcriptomic, and stress-associated trajectories. A diagnostic platform combining fluorescence lifetime imaging microscopy, long-read sequencing, and digital polymerase chain reaction may improve early mechanistic classification, help identify embryos with possible reversibility, and reduce uncertainty in embryo selection during in vitro fertilization. Full article

During eukaryotes evolution, mitochondrial DNA (mtDNA) fragments integrate into nuclear genomes, forming nuclear mitochondrial DNA sequences (Numts). Tortricidae (Lepidoptera), a species-rich and economically critical family, lacks systematic characterization of Numts, which hinders reliable molecular research. Here, we systematically characterized Numts in 27 Tortricidae species spanning two subfamilies via genome download, mitochondrial genome annotation, and Numt identification and characterization. With each species’ mtDNA as query, Numt identification was performed with an E-value threshold of 10⁻⁴ and a sequence similarity cut-off of >60%, with a minimum length of 50 bp to exclude spurious hits. Results showed that all species contained Numts, with copy numbers varying drastically (9–208). Numt numbers positively correlated with nuclear genome length, but not mitochondrial genome length. Numts insertion flanking regions had significantly higher AT content than nuclear genome, indicating the insertion preference for AT-rich regions. Numts were predominantly derived from the mitochondrial cox1 gene, highlighting the risk of co-amplification when cox1 is used as a DNA barcode for species identification or phylogenetic studies. This study represents a systematic charaterizition of copy number, length distribution, insertion sequence preferences, and mitochondrial gene origins of Numts in Tortricidae, offering valuable references for refining molecular systematics, comparative genomics, and pest management in Tortricidae and related lepidopteran groups. Full article

Background/Objectives: The gut–brain axis is increasingly recognized as a critical modulator of cognitive function. This study investigated the neurotoxic effects of combined exposure to bacterial lipopolysaccharide (LPS) and the antiretroviral drug zidovudine (ZDV) in a mouse model, and evaluated the protective potential of two probiotic interventions: Bacillus subtilis and a mixture of lactobacilli. Methods: Cognitive function was assessed using the Morris water maze (MWM). Gut microbiota composition was analyzed by 16S rRNA sequencing, and intestinal morphology was examined histologically. Gene expression of neuroinflammatory markers and mitophagy-related genes in brain tissue was quantified by RT-PCR. Plasma levels of cell-free mitochondrial DNA (cf-mtDNA) were measured as a marker of mitochondrial damage. Results: Combined LPS + ZDV exposure induced systemic inflammation, impaired spatial memory, damaged the intestinal mucosa, and caused dysbiosis characterized by an increase in pro-inflammatory Muribaculaceae. In the brain, LPS + ZDV significantly upregulated Tnfa expression, confirming neuroinflammation. Bacillus subtilis administration prevented cognitive deficits, maintained Tnfa at control levels, and significantly reduced Il1b and Il6 expression compared to the LPS + ZDV group. This was accompanied by activation of the PINK1/PTEN-dependent mitophagy pathway, prevention of cf-mtDNA release, and restoration of gut microbial diversity. In contrast, the Lactobacilli mixture not only failed to improve outcomes but was associated with exacerbated intestinal damage, more pronounced cognitive dysfunction, and no reduction in neuroinflammatory markers. Conclusions: Combined exposure to LPS and ZDV induces gut–brain axis dysfunction characterized by neuroinflammation, cognitive impairment, intestinal damage, and dysbiosis. Bacillus subtilis effectively preserves cognitive function through activation of PINK1/PTEN-dependent mitophagy and suppression of neuroinflammation, highlighting its potential as a therapeutic candidate for cognitive impairments associated with gut–brain axis dysfunction. The contrasting effects of the lactobacilli mixture underscore the critical importance of strain-specificity in probiotic interventions. Full article

Background/Objectives: The combination of hearing loss and visual impairment in a single patient strongly suggests a genetic aetiology. However, after conventional testing, a considerable proportion of deafblindness cases remain without a genetic diagnosis. The aim of this study was to address this diagnostic gap. Methods: We developed an enhanced exome strategy that uses a whole-exome backbone complemented by spike-in capture probes for (i) low-coverage coding segments and clinically validated, non-coding regions (including deep intronic splice-altering sites and untranslated exonic sequences) across 659 genes associated with hearing loss and/or visual impairment, and (ii) mitochondrial DNA. Results: With 66.6 million paired-end reads per sample, this methodology achieved coverage of at least 20 reads per base at 99.3% of target coding and non-coding positions of genes associated with deafness and/or blindness, as well as 98.8% of the whole exome. The enhanced exome approach correctly identified the genetic variants causative of deafness and/or blindness in 10 out of 10 cases with a previously known genetic cause, in 3 out of 10 additional cases that remained undiagnosed after extensive panel sequencing, and in 4 out of 4 cases that had not been genetically studied before. Comparison of the performance of two commercial bioinformatics platforms for enhanced exome interpretation revealed that eVAI consistently prioritised causative variants higher than, or as high as, VarSome Clinical, resulting in a tendency toward shorter interpretation times using the former. Both platforms offered the same diagnostic yield and both failed to correctly call one of the causative variants. Conclusions: In an era where many centres operate exome analysis through virtual panels, enhanced exome sequencing leverages the advantages of whole-exome and custom panel sequencing: it provides panel-like sensitivity for clinically actionable loci, while offering the flexibility to periodically reanalyse data and discover candidate genes. Full article

Background/Objectives: The OPA1 gene encodes a dynamin-related GTPase essential for mitochondrial fusion. Variants in OPA1 are a major cause of autosomal dominant optic atrophy (DOA). A subset of DOA patients exhibits hearing loss, often manifesting as auditory neuropathy spectrum disorder (ANSD). In this study, we aimed to describe the frequency of OPA1-related hearing loss in a large cohort of patients with hearing loss and to explore the genotype–phenotype correlations and appropriate interventions. Methods: A total of 18,475 Japanese patients with hearing loss were recruited. Targeted massively parallel sequencing of 158 deafness-related genes was performed, and individuals with OPA1 variants were identified. Clinical data, including age of onset, audiological findings, and systemic features, were retrospectively reviewed. Results: Ten individuals from eight independent families carrying OPA1 variants were identified. Three variants were classified as pathogenic or likely pathogenic, while five were variants of uncertain significance. Hearing loss was typically post-lingual in onset and progressive, with predominantly mild-to-moderate severity. Missense variants tended to be associated with DOA-plus phenotypes and ANSD. Five patients obtained only limited benefit from hearing aids, whereas one patient who received a cochlear implant achieved good speech perception. Conclusions: OPA1 is a rare causative gene for hearing loss and is frequently associated with the ANSD phenotype. Affected individuals exhibited phenotypic heterogeneity, which may reflect incomplete penetrance or the influence of mitochondrial DNA-related factors. Full article

Background/Objectives: Mitochondrial DNA (mtDNA) is an important resource for understanding human ancestry, population diversity, and the molecular mechanisms of mitochondrial diseases. However, analyzing mtDNA thoroughly often requires advanced bioinformatics skills and command-line knowledge. To address this challenge, we created Mitochondrial Genome Explorer (MitoGEx), a user-friendly computational pipeline optimized for human mtDNA analysis that combines multiple mtDNA analysis modules within a single graphical user interface. Methods: The platform simplifies key analytical steps, such as quality control, sequence alignment, alignment quality assessment, variant detection, haplogroup classification, and phylogenetic reconstruction. Users can choose between Quick and Advanced modes, which offer default settings or customizable options based on their analysis needs. To demonstrate its effectiveness, we analyzed 15 whole-exome sequencing (WES) samples from Songklanagarind Hospital using MitoGEx. Results: The sequencing data were of high quality, with over 92 percent of bases scoring above a Phred score and consistent GC content across all samples. Variant detection using the GATK mitochondrial pipeline and annotation with ANNOVAR and the MitImpact database revealed multiple high-confidence variants. Haplogroup classification with Haplogrep 3 and phylogenetic analysis with IQ-TREE 2 confirmed diverse maternal lineages within the cohort. Conclusions: Taken together, MitoGEx facilitates mitochondrial genome analysis in a reproducible and accessible manner for both research and clinical bioinformatics applications. The analytical results produced by MitoGEx are concordant with those obtained using standalone bioinformatic tools, demonstrating analytical correctness. By integrating all analysis steps into a single automated workflow, MitoGEx reduces execution time and limits human error inherent to manual, multi-step pipelines. Full article

Background/Objectives: Mitochondrial DNA (mtDNA) analysis is an essential tool for human identification in contexts such as disaster victim identification (DVI) and missing persons cases, where the remains may be highly degraded or even skeletonised. Traditionally, capillary electrophoresis (CE)-based Sanger sequencing has been the standard method for analysing the mtDNA control region. With the development of massively parallel sequencing (MPS) technologies, mtDNA sequencing using MPS offers advantages over traditional Sanger sequencing, such as increased sensitivity, higher throughput, and less sample consumption. The Ion Chef™ and Ion S5™ XL system from Thermo Fisher Scientific represents one such MPS system. Methods: We conducted an internal validation study evaluating key parameters including (a) concordance, repeatability and reproducibility; (b) potential cross-contamination; (c) sensitivity; (d) effects of library pooling on read depth; and (e) mixture sample analysis. Additionally, to mimic samples typically encountered during forensic investigations, case type samples were also used to evaluate the performance of this workflow. While the entire mitochondrial genome was sequenced in this validation study, considering that the international guidelines for full mtDNA genome analysis and interpretation have yet to be fully updated, our analysis, interpretation and subsequent implementation are limited to the control region only. Results: The results obtained demonstrated the reliability, sensitivity and reproducibility of this MPS workflow. Conclusions: This internal validation study supports the implementation of this workflow in our laboratory for the analysis of forensic casework samples. Full article

Pancreatic cancer (PC) is a highly aggressive malignancy characterized by limited opportunities for early diagnosis and poor clinical outcomes, underscoring the need for minimally invasive biomarkers to improve detection and patient stratification. Given emerging evidence that mitochondrial DNA (mtDNA) alterations reflect cancer-related biological processes, this study investigated whether blood-derived mtDNA profiles could provide clinically relevant information in PC. In this exploratory study, whole-blood mtDNA from 33 PC patients and 10 healthy individuals were analyzed using next-generation sequencing to assess single-nucleotide variants (SNVs), allele frequencies, and mtDNA copy number. A total of 252 unique mtDNA SNVs were identified, including variants exclusive to PC patients, variants unique to controls, and variants shared between groups. While the overall SNV burden did not differ significantly between groups, PC patients showed distinct mutation distributions and allele frequency patterns, with cancer-exclusive variants occurring predominantly at low allele frequencies. Mutation hotspots were observed in the ND5, COI, and D-loop regions, implicating genes involved in oxidative phosphorylation and mtDNA maintenance. Although mtDNA copy number did not differ significantly between groups, greater variability was observed among PC patients and was associated with differences in survival outcomes. Overall, these findings indicate that blood-based mtDNA profiling captures biologically relevant variation associated with PC and supports further development of integrated mtDNA-based approaches for improved risk assessment and patient stratification. Full article

The teak defoliator, Hyblaea puera, native to South Asia and Southeast Asia (e.g., India, Laos, and Myanmar), has recently caused frequent outbreaks in mangrove forests across Guangdong, Guangxi, and other regions of China. Its larvae feed extensively on the leaves of Avicennia marina, severely threatening local mangrove ecosystems. However, accurate morphological identification of H. puera across its eggs, larvae, and pupae remains challenging. Therefore, the development of rapid molecular detection methods is essential for effective pest identification and monitoring, thereby supporting timely management interventions. In this study, mitochondrial protein-coding genes (PCGs) were analyzed from H. puera and related species were analyzed. Sliding window analysis was conducted to estimate nucleotide diversity (Pi), leading to the selection of the cytochrome c oxidase subunit I (COI) gene as the optimal target. Species-specific primers were designed based on the H. puera COI sequence, and two molecular detection assays—SS-PCR and LAMP—were developed. Both assays exhibited high specificity, stability, and sensitivity, successfully amplifying target fragments from H. puera across all tested geographic populations and different developmental stages. The limit of detection of the SS-PCR method was 83 fg/µL DNA, while that of the LAMP method reached 8.3 fg/µL DNA. The newly developed assays offer reliable and robust tools: the SS-PCR method is suitable for precise, large-scale detection in laboratory settings, whereas the LAMP assay is preferable for rapid, field-based detection of H. puera. These methods contribute to the early detection and effective management of H. puera populations, thereby safeguarding mangrove ecosystems. Full article

Horizontal transfer of mitochondrial DNA into the nuclear genome generates nuclear mitochondrial sequences (NUMTs), which serve as molecular fossils reflecting long-term mitochondrial–nuclear interactions and genome evolution. However, the biological mechanisms governing NUMT integration, retention, and evolutionary fate remain incompletely understood in domesticated animals. Here, using the latest pig reference genome assembly (Sscrofa11.1), we present a comprehensive genome-wide characterization of NUMTs in pigs and provide new insights into their genomic distribution and evolutionary constraints. We identified 513 high-confidence NUMTs, of which 460 were chromosomally mapped, accounting for 0.0106% of the nuclear genome. Beyond increased detection, our analyses reveal that pig NUMTs exhibit non-random origins, preferentially integrate into genomic regions under weak selective constraint, and are frequently associated with repetitive elements, consistent with a DNA repair-mediated insertion mechanism. NUMTs predominantly occur as short, fragmented sequences and show signatures of long-term neutral evolution, while insertions disrupting coding sequences are strongly selected against. Synteny-based analyses further identified clustered NUMT regions and duplicated NUMTs, suggesting secondary genomic duplication events following initial integration. Comparative analysis with the earlier Sscrofa10.2 assembly demonstrates that improved genome quality substantially enhances NUMT detection, particularly in repetitive and GC-rich regions, clarifying previously ambiguous sequence-context associations. Together, this high-quality pig NUMT map provides a robust foundation for future functional, evolutionary, and population-level investigations and contributes to the conservation and utilization of pig genetic resources. Full article

Corydalis impatiens (Papaveraceae) is a traditional Tibetan medicinal plant (“Pa Xia Ga”) whose mitochondrial genome evolution remains unexplored, particularly in the context of high-altitude adaptation. This study presents the first complete mitochondrial genome sequence of an alpine Corydalis species to establish a comparative framework with the lowland congener C. pauciovulata for investigating environment-associated mitochondrial evolution. Using Illumina sequencing and reference-guided assembly, we characterized a 688,959 bp circular genome containing 74 genes, with GC content variations reflecting functional compartmentalization—elevated in structural RNA genes (tRNAs: 51.24%; rRNAs: 52.79%) versus protein-coding genes (44.19%). We identified 719 RNA editing sites concentrated in NADH dehydrogenase genes, suggesting post-transcriptional optimization of respiratory complex I under hypoxic conditions. The genome harbors 50 dispersed repeats (7.50%) and 67 SSRs with A-rich predominance, providing species-specific markers for authenticating “Pa Xia Ga” in Tibetan medicine quality control. Phylogenomic analysis confirms close affinity with C. pauciovulata while resolving intrageneral relationships within Ranunculales. These findings establish a dual-reference system for distinguishing conserved genus-level features from altitude-associated adaptations, enabling future comparative mitogenomics across the 465-species genus and supporting DNA-based medicinal plant identification. Full article

The identification of species complexes in freshwater snails remains challenging due to limited diagnostic morphological characters and incomplete taxonomic knowledge in many taxa. Within the family Bithyniidae, species have traditionally been classified using shell morphology and genital anatomy to distinguish intraspecific variation from interspecific differences. However, extensive morphological plasticity has hindered reliable species delimitation, and the presence of cryptic diversity further complicates taxonomy. Recent DNA barcoding studies of Hydrobioides have provided evidence of such cryptic diversity, highlighting the need for taxonomic reassessment within the genus. In the present study, we examined morphological variation in Hydrobioides nassa from Thailand in conjunction with mitochondrial DNA sequence data. Molecular phylogenetic analyses based on cytochrome c oxidase subunit I (cox1) sequences revealed three well-supported genetic lineages within H. nassa, accompanied by high levels of pairwise genetic divergence. Morphological comparisons of shell, operculum, and radular characters further supported differentiation among these lineages, although some characters showed overlap. While Hydrobioides has previously been regarded as comprising a single morphologically defined species, our results demonstrate that H. nassa represents a complex of genetically distinct lineages with subtle but consistent morphological differences. This study highlights the importance of integrating molecular approaches with traditional morphological analyses to improve taxonomic resolution and to better understand biodiversity within freshwater snail groups exhibiting cryptic diversity. Full article