Search Results (557)

Corydalis ophiocarpa is a medicinally valuable plant, noted for its abundant alkaloid content. Despite its significance, the mitochondrial (mt) genome of this plant has not been characterized, which impedes both the phylogenetic understanding within the Corydalis genus and the comprehension of its full genetic potential. In this research, we successfully assembled the complete mitogenome of C. ophiocarpa by employing a hybrid method that integrates Oxford Nanopore long reads with Illumina short reads. The assembled genome forms a circular structure of 600,064 bp, with a GC content of 46.49%, and includes 63 genes, comprising 40 unique protein-coding genes (PCGs), 20 tRNAs, and three rRNAs. Through assembly and coverage analysis, we identified a 6383 bp forward repeat associated with a contig having approximately double the depth, indicating a repeat-mediated multipartite structure where the main circle may coexist with two smaller subgenomic forms. We discovered 775 C-to-U RNA editing sites across the 40 PCGs, with 95.4% being non-synonymous and favoring hydrophobic amino acid substitutions, particularly in Complex I subunits. Furthermore, we identified sixteen mt plastid DNA fragments constituting 2.43% of the mitogenome, a proportion more than double that found in the closely related C. saxicola. Phylogenetic analysis confirms that C. ophiocarpa is most closely related to C. saxicola, with C. pauciovulata as another close relative. This study presents the first complete mitogenome of C. ophiocarpa, providing a genomic basis for investigating the relationships between mt genome structure, post-transcriptional regulation, and specialized metabolism in the Corydalis genus. Full article

The systematics of white-tailed deer (Odocoileus virginianus) has been controversial. Some mammalogists consider the white-tailed deer to be a single species, whereas others consider it to consist of multiple species. To help resolve the controversy, we sequenced mitochondrial cytochrome B (mtCyt-b) in samples collected from 83 Neotropical white-tailed deer. Furthermore, we analyzed mitogenomes of samples collected from 19 white-tailed deer. There were five main results, as follows: (1) Phylogenetic analyses with the mtCyt-b dataset showed the existence of eight groups of O. virginianus, three in North and Central America and five in South America. It was hypothesized from different analyses that a Central American O. virginianus population generated the white-tailed deer populations in South America. (2) The haplotype temporal diversification within O. virginianus occurred during the Pleistocene. With the mitogenome dataset, it was dated to have occurred approximately 2.2 mya, using both Bayesian inference and haplotype networks. (3) All of these O. virginianus groups showed elevated levels of mitochondrial genetic diversity for the mtCyt-b dataset, with the exception of the Ecuadorian population (4) Some groups of O. virginianus yielded significant evidence of female population expansions with the mtCyt-b dataset. (5) Although the genetic heterogeneity among these O. virginianus groups was significant, the genetic distances were relatively small. Provisionally, the karyotypic differences between North American and Colombian specimens were very small; therefore, until further karyotypic studies demonstrate otherwise, we consider the existence of a single species of O. virginianus. Because mtDNA genomes have only one quarter of the effective number of autosomal nuclear genes, this generates relatively rapid coalescence times, which can inflate estimates of divergence among populations. Therefore, it is very important to soon sequence the nuclear genes for the different geographic assemblages of O. virginianus found. Full article

Background: The transfer of a nucleus from one oocyte to another offers patients harbouring high levels of mitochondrial DNA mutation and sufferers of frequent fertilisation failure or early embryonic arrest the potential to have healthy children. However, a small amount of mtDNA is carried over with the nucleus as the transfer takes place. Consequently, we still need to distinguish between the effects of the carryover and the transfer of a nucleus itself from a mature oocyte. Methods: To overcome this, we analysed a series of hatching stage blastocysts generated using metaphase II spindle transfer and mitochondrial supplementation. The latter approach also introduces a small amount of mtDNA into the oocyte as fertilisation takes place. For both manipulations, an autologous approach was used to overcome the effects of third-party transfer. Results: We then compared the changes in global gene expression between the two groups. We found that the nuclear transfer process affected a number of gene networks and pathways. These included metabolic, cell cycle, inflammatory and immune, and epigenetic responses. A comparison with earlier stage blastocysts did not suggest that the cause was due to developmental delay. Conclusions: Critically, these changes could affect offspring health and well-being as is the case following somatic cell nuclear transfer. Full article

DNA methylation, the covalent addition of methyl groups to cytosine (5mC) or adenine (6mA) in DNA, is a fundamental mechanism of epigenetic inheritance conserved from bacteria to humans. Fungi provide a uniquely informative window into the evolutionary logic of methylation systems. Spanning more than 1 billion years of diversification, the kingdom encompasses species that have lost cytosine methylation entirely, lineages that use 5mC to silence transposons and drive the irreversible genome-defense process known as repeat-induced point mutation (RIP), and early-diverging lineages, in which 6mA has emerged as a prominent chromatin mark. The methyltransferases underlying these strategies (DIM-2, RID, DNMT1-RFD, DNMT5, and the MT-A70 complex) and the recently characterized demethylases Dmt1 and CcTet are structurally and mechanistically distinct from their mammalian counterparts. Here we review the mechanisms, targets, and biological functions of fungal DNA methyltransferases and demethylases, incorporating cryo-EM structural insights into DIM-2 and DNMT5 catalysis, analyses of DNMT gene loss as a continuous evolutionary process, the antiviral role of DIM-2 in vegetative hyphae, and the emerging model of 6mA as a heritable regulatory mark in early-diverging lineages. By integrating these advances, this review offers the updated and comprehensive account of DNA methylation across fungi. Full article

The field of mitoepigenetics involves the investigation of modifications in mitochondrial DNA (mtDNA), genomic DNA that encodes mitochondrial proteins, and the expression of RNAs that regulate mitochondrial gene expression but do not alter the DNA sequence. This area of research is growing rapidly and has substantial relevance to male mammalian fertility. Among the known mitoepigenetic mechanisms, mitochondrial microRNAs (mitomiRs) have attracted substantial attention due to their potential roles in modulating mitochondrial gene expression in response to environmental stressors. Since many problems with male fertility are known to result from environmental factors, there has been increasing interest in studying epigenetic mechanisms that contribute to male reproductive function. This review explores the current literature regarding different mitoepigenetic mechanisms and their implications for male mammalian fertility, focusing primarily on the known and potential involvement of mitomiRs in model species and humans. Understanding mitoepigenetics may contribute to the development of non-invasive diagnostic biomarkers and individualized therapeutic approaches to male infertility due to their stability in body fluids, tissue specificity, and sensitivity to disease states. Full article

Background and Objectives: Although clinically useful, homologous recombination deficiency (HRD) testing has recently been more broadly adopted in ovarian cancer (OC) management. The VALIDATE study evaluated HRD status and treatment patterns in patients with newly diagnosed advanced OC in Bulgaria to better understand HRD prevalence and disease management. Materials and Methods: This real-world, observational, multi-centre, medical chart review study included 100 adult patients with HRD testing results available at study entry. Data collected at least 30 days after HRD results and 6 months later were descriptively analysed in the full cohort and subgroups (HRD, BRCA mutation, and genomic instability score [GIS]). Results: Mean age at diagnosis: 61.3 years; stage III: 51.0%, prevalence of HRD+ 58.0% (95% confidence intervals [CI] 47.7–67.8%) and HRD− 42.0% (95% CI 32.2–52.3%). Among the 58 HRD+ patients, 20 (34.5%) were BRCA+, whereas 38 (65.5%) were BRCA−, and 52 (89.7%) were GIS+, and 6 (10.3%) GIS−. Overall, platinum–taxane chemotherapy plus antiangiogenics was the most common front-line (FL) treatment (77.0%), regardless of subgroups (range: 66.7–85.0%). Six months later, 81 patients were alive, and 73 (90%) started maintenance therapy (MT). Antiangiogenic monotherapy (32.0%) and antiangiogenic plus PARP inhibitor (34.0%) were the most common MTs. The latter was also common across subgroups (range: 33.3–60.5%), except for HRD− (61.9% received antiangiogenic monotherapy). Conclusions: In this dataset, more than half of advanced OC patients had HRD+ status. Our study provides relevant insights into recent clinical practice patterns in advanced OC in Bulgaria that could serve as an anchor for future, more robust research in this field. Full article

Horizontal Gene Transfer (HGT) is a hallmark of the evolution of parasitic plants, facilitated by the haustorial connection. While mitochondrial HGT is widespread, the extent of nuclear HGT and the long-term retention of foreign genetic material in holoparasitic lineages remain poorly understood. This study explores the genomic architecture of Prosopanche americana (Hydnoraceae), a non-photosynthetic holoparasite currently specialized on Fabaceae. Through a comparative phylogenomic approach integrating draft mitochondrial genomes (mtDNA) and nuclear transcriptomes of P. americana, we identified a multi-layered landscape of foreign DNA. The mtDNA of P. americana contains 18 foreign regions (>500 bp) primarily derived from Solanales, Malvales, and Fabales. Notably, 13 of these regions are shared with P. panguanensis, indicating they were acquired in their common ancestor before speciation and ecological shift. In the nuclear genome, we identified 303 horizontally acquired transcripts (99 orthogroups) with high confidence. Functional analysis revealed an enrichment of foreign genes involved in metabolic pathways and plastid functions (e.g., photosystems and thylakoids) exclusively derived from the ancestral host order Solanales. Our results demonstrate that the genome of P. americana acts as a “molecular fossil,” preserving evidence of past ecological interactions with diverse host lineages. The disparity in HGT footprints between the current host (Fabaceae) and ancestral hosts suggests a period of high genomic plasticity followed by host specialization, providing new insights into the timing and dynamics of horizontal gene flow in holoparasitic Piperales. Full article

Ultraviolet (UV) radiation from the sun causes adverse skin changes such as premature aging. UV-induced mitochondrial DNA (mtDNA) alterations, including deletions, contribute to photoaging and cellular dysfunction. While the most frequent mtDNA rearrangement is the common deletion (CD), characterized by the loss of nearly one-third of the genome (4977 bp), detailed knowledge of mechanisms governing UV-mediated initiation of the CD and mitigation strategies are lacking. Here, we investigated how increasing UV exposure increases CD levels in human skin fibroblasts via cellular reactive oxygen species (ROS) formation and mtDNA oxidation and demonstrated that antioxidant preconditioning of cells prevents UVA-induced CD accumulation. Conversely, UVB exposure induced cyclobutane pyrimidine dimers (CPDs) without affecting ROS, suggesting an ROS-independent pathway. Using a 3D full-thickness human skin model, we confirmed UVA-dependent CD formation in both the epidermis and dermis. RNA-Seq analysis of UVA-exposed fibroblasts revealed upregulation of mitochondrial DNA replication genes and downregulation of mtDNA repair genes. These findings provide insight into how UVA and UVB differ in detrimental effects on mtDNA, with UVA impacting mtDNA maintenance and transcription via a ROS-dependent mechanism, and provide a physiologically relevant platform to evaluate potential interventions. Full article

Wildlife trafficking poses a severe threat to global biodiversity and ecosystem stability, necessitating robust forensic tools for tracing the origins of illegally traded taxa. In this study, we developed a method of single-nucleotide polymorphism (SNP)-based molecular markers to enable precise geographical traceability of four animal species native to China: the Tibetan macaque (Macaca thibetana), brown eared pheasant (Crossoptilon mantchuricum), blue eared pheasant (Crossoptilon auritum), and Chinese pangolin (Manis pentadactyla). We studied these four species because their DNA is characterized by distinct population genetic structure, they are subjected to illegal trafficking, and given their diverse evolutionary histories, this allowed us to assess the general applicability of our forensic genetic framework in reducing wildlife crime. Based on whole-genome resequencing data from 26 Tibetan macaques, 51 eared pheasants and 42 Chinese pangolins, we performed population genetic analyses to elucidate their genetic structure and identify population-specific loci. The results indicated that all samples from these four species showed clear genetic differentiation and distinct clustering, allowing us to design primers to facilitate PCR-based traceability. We also assessed the utility of mitochondrial DNA (mtDNA) for tracing Tibetan macaques and both species of eared pheasants. We found that traceability accuracy using mtDNA was lower than when using SNPs. Our research offers a SNP-based traceability framework that accurately determines the geographical origin of wildlife samples to the genetic population level, and this provides a powerful tool for combating illegal trade and aiding conservation efforts. 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: 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

The black carp (Mylopharyngodon piceus) is an ecologically and economically important freshwater fish native to China and neighbouring regions, but its wild stocks have declined sharply in recent decades. We analysed mitochondrial cytochrome b (Cyt b) sequences from 100 individuals collected in 2008–2009 from four Yangtze River, two Pearl River and one Red River populations to assess genetic diversity and structure as a pre-ban baseline for maternal lineages. Sixteen polymorphic sites defined 17 haplotypes, with a single dominant haplotype (Hap2) shared across all populations. Haplotype diversity was high but nucleotide diversity low, and neutrality tests together with mismatch-distribution analyses were consistent with a recent Late Pleistocene demographic expansion. Pairwise FST values ranged from negligible differentiation among middle–lower Yangtze populations to pronounced differentiation between the upstream Yangtze population (SS) and middle–lower populations and between the Yangtze and the combined Pearl–Red basins, whereas Pearl and Red River populations showed no significant divergence and high mitochondrial homogeneity, consistent with substantial historical connectivity. Overall, the Cyt b data indicate low mitochondrial diversity and shallow but significant inter-basin structuring, providing preliminary mtDNA-based evidence that Yangtze and Pearl–Red populations represent candidate conservation and management units, and highlighting the need for nuclear genomic markers and contemporary sampling to refine drainage-scale units and evaluate recent management effects. Full article

Understanding the complex molecular mechanisms behind gynecological cancers is crucial, as these diseases pose significant challenges to women’s health and are frequently diagnosed at advanced stages. Various genetic, epigenetic, and metabolic alterations play a vital role in tumor development, metastasis, and therapy. Exploring mitochondrial dysfunction and the role of lncRNAs may provide essential insights into how tumor cells evade apoptosis, alter their metabolic pathways, and adapt to stress. In gynecological malignancies, nuclear lncRNAs contribute to tumor progression, treatment resistance, and metastasis through mechanisms that include chromatin remodeling, microRNA modulation, and regulation of mitochondrial dynamics. More recently, the emerging role of mt-lncRNAs, derived from the mitochondrial genome, has attracted attention for their involvement in retrograde signaling, mitochondrial respiration, and regulation of apoptosis. Dysregulation of mt-ncRNAs may contribute to tumor bioenergetic reprogramming, mitochondrial integrity, and nuclear gene expression. The objective of this review is to consolidate the current understanding of the regulatory mechanisms of mitochondrial lncRNAs in ovarian, cervical, and endometrial cancers, thus identifying new opportunities of research. A thorough elucidation of the role of mitochondrial lncRNAs in mitochondrial–nuclear communication may facilitate the development of new interventions in gynecological oncology, highlighting the potential of these molecules as diagnostic biomarkers and therapeutic targets. Full article

Mitochondrial biogenesis requires coordinated expression from both nuclear and mitochondrial genomes. To understand the consequences of mitochondrial genome loss, we generated a mitochondrial DNA-depleted line (crm⁻) in Chlamydomonas reinhardtii via long-term ethidium bromide treatment. We then examined how mtDNA disruption affects mitochondrial ultrastructure, chloroplast function, and the mitochondrial transcription termination factor (mTERF) gene family. Our results reveal that mitochondrial dysfunction is associated with severe organelle remodeling, including mitochondrial elongation, matrix condensation, and cristae collapse. Consequently, mitochondria reduce the electron sink capacity which appears to over-reduce the chloroplast electron transport chain, correlating with causing damage to photosystem II (PSII), as indicated by higher plastoquinone PQ redox state and PSII excitation pressure and lower non-photochemical quantum yield [Y(NPQ)]. Furthermore, we identified and characterized eight nuclear-encoded mTERF genes in C. reinhardtii (CrmTERFs). Phylogenetic analysis grouped them into three clades with potential functional conservation. Collinearity analysis suggested potential evolutionary relationships between mTERF genes in Chlamydomonas and Marchantia polymorpha. Gene ontology annotation linked CrmTERFs to transcription termination and RNA biosynthesis regulation. Additionally, in silico prediction identified twelve putative miRNAs targeting seven of the eight CrmTERFs, with CrmTERF3 as the only exception, providing candidates for future experimental validation. This study provides the first comprehensive analysis of the nuclear encoded mTERF gene family in Chlamydomonas and demonstrates that mtDNA loss is correlated with mTERF genes expression, as well as mitochondrial structure and chloroplast photoprotective impairments. These findings suggest a potential role for CrmTERFs in mitochondrial retrograde signaling and organellar crosstalk, though functional validation is required to establish causality. Full article