Search Results (1,708)

Myocardial injury is a critical determinant of prognosis in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection; however, its underlying mechanisms remain incompletely understood. In this study, we examined the effects of SARS-CoV-2-derived RNA fragments on human cardiomyocytes. We identified a 19-nucleotide sequence within the viral genome that shares complete sequence homology with the human F1F0 ATP synthase subunit alpha gene (ATP5A). This sequence was found to associate with Argonaute 2 (AGO2) and downregulate ATP5A expression via a mechanism analogous to RNA interference. Consequently, oxidative phosphorylation was suppressed in cardiomyocytes, leading to impaired myocardial maturation and the emergence of heart failure-like phenotypes. Notably, exosome-mimetic liposomal delivery of this RNA fragment to cardiomyocytes reproduced the ATP5A-suppressive effect. These findings suggest that SARS-CoV-2-derived RNA fragments may contribute to myocardial injury through the siRNA-like modulation of mitochondrial gene expression. Further validation in animal models and patient-derived materials is warranted. Full article

Cellular senescence is a key mechanism of aging. Senescent cells negatively affect the function of tissues and organs, significantly contributimg to the aging of the organism. Functional and structural characteristics of senescent cells, such as genomic changes and cell cycle arrest, lysosome and mitochondrial dysfunction, and production of SASP factors, are promising therapeutic targets in the context of healthy longevity. The present review was designed to characterize the features of senescent cells in order to discuss current methods and problems of geroprotective therapy and perspective factors for the development of new strategies of anti-aging treatment. Publications were searched based on the analysis of articles containing the keywords “senescent cells, aging, senolytic therapy, SASP, mitochondrial dysfunction” in the PubMed and Scopus databases up to March 2025. Full article

Melicope pteleifolia (Rutaceae) is a shrub or tree with high medicinal value. Although the physical features of M. pteleifolia are evident, the mitochondrial (mt) genome has yet to be investigated, and its evolutionary relationship within Rutaceae is unclear. The organelle genomes of M. pteleifolia were constructed using Nanopore and Illumina sequencing data. The circular mt genome is 780,107 base pairs (bp) long, with a GC content of 44.85%. It has 66 genes, consisting of 33 protein-coding genes (PCGs), 30 tRNA genes, and 3 rRNA genes. The length of the chloroplast (cp) genome was 158,987 bp, containing 88 PCGs, 37 tRNAs, and 8 rRNAs. The mtDNA and cpDNA contained 507 and 353 repetitive sequences, respectively. RNA editing sites were abundant in M. pteleifolia organelle genomes, including 323 sites in mtDNA and 260 sites in cpDNA. Phylogenetic research using the cp and mt genomes of M. pteleifolia and nine additional species of the Rutaceae family precisely delineates its evolutionary and taxonomic position. Ka/Ks and nucleotide diversity indicated that the majority of the PCGs in the mitochondrial genome had experienced negative selection. These findings provided comprehensive information on the M. pteleifolia mitogenome for studying phylogenetic relationships in Rutaceae, with chloroplast-derived sequences providing critical evidence for inter-organellar genome evolution. Full article

Background/Objectives: The genus Vitis comprises approximately 70 species with high genetic diversity, among which Vitis vinifera is the most economically significant. Despite numerous studies on the genetic characterizations of V. vinifera, selecting optimal chloroplast DNA barcoding regions for intraspecific differentiation remains unresolved. Most studies have focused on nuclear markers (SSRs, SNPs) or widely used chloroplast loci (e.g., matk, rbcl), which have shown limited resolution at the subspecies level. In this study, the complete chloroplast genomes of 34 V. vinifera accessions from different varieties and hybrids (vinifera, sylvestris, caucasica, and labrusca) were analyzed to identify the key genomic regions for DNA barcoding. Methods: Using bioinformatics tools, we assessed the genome structure, nucleotide variability, microsatellites, codon usage bias, and phylogenetic relationships among the investigated varieties. Results: The chloroplast genomes displayed a quadripartite structure, with lengths ranging from 160,906 to 160,929 bp and a guanine–cytosine (GC) content of ~37.4%. Phylogenetic analysis revealed an unusual position for VV-5 vini and VVVL-3 lab, suggesting potential taxonomic misclassification or hybridization effects. A single locus showed low discrimination power, but the concatenation of five loci (ccsA-trnN-GUU, rpl16, rpl2-rps19, rpoC2, and trnM-CAU) exhibited significantly improved resolution (44.11% K2P), surpassing traditional markers. Conclusions: This study addresses the gap in the literature regarding the use of concatenated chloroplast loci for subspecies research; the results validate these markers across a broader range of Vitis accessions and integrate nuclear and mitochondrial data to achieve a more comprehensive understanding of the evolutionary history and genetic diversity of V. vinifera. Full article

Red algae are recognized for their health-promoting bioactive substances and dietary fibers, making them important as functional food. In order to identify species and determine phylogenetic relationships, mitochondrial genes serve as important markers. Thus, this study sequenced the complete mitochondrial genome of Ahnfeltiopsis flabelliformis, compared with Phyllophoraceae species, and performs phylogenetic analysis to reveal its evolutionary position. The genome is 25,992 bp long, has 71.3% of biased AT content, and comprises 24 protein-coding genes (PCGs), 22 tRNA, and three rRNA genes. The overall base composition of its mitochondrial genome was 37.4% for A, 33.9% for T, 14.7% for G, 14.0% for C and 28.7% for GC. The gene content, annotation, and genetic makeup are identical to those of Phyllophoraceae species. Phylogenetic study based on the complete mitochondrial genome and shared mitochondrial genes revealed that the six Phyllophoraceae species form a well-supported clade. Within this clade, A. flabelliformis groups with Gymnogongrus griffithsiae, and together they form a distinct subclade including four species of the Mastocarpus. The results indicate that A. flabelliformis shares a closer evolutionary relationship with G. griffithsiae than with Mastocarpus species. Future research on Ahnfeltiopsis is necessary to comprehend the evolutionary history and phylogenetic relationships among species in this genus. Full article

Objectives: Codon usage bias is a fundamental feature of gene expression that can influence evolutionary processes and genetic diversity. This study aimed to investigate the mitochondrial codon usage characteristics and their driving forces in three Medicago species: Medicago polymorpha, Medicago sativa, and Medicago truncatula. Methods: The complete mitochondrial genome sequences of the three species were downloaded from GenBank, and 21 shared coding sequences were screened. Codon usage patterns were analyzed using CodonW 1.4.2 and CUSP software. Key parameters, including the relative synonymous codon usage (RSCU), effective number of codons (ENC), codon adaptation index (CAI), codon bias index (CBI), and frequency of optimal codons (Fop), were calculated. Phylogenetic trees and RSCU clustering maps were constructed to explore evolutionary relationships. Results: The GC contents of the mitochondrial genomes followed the order of GC1 > GC2 > GC3. ENC values averaged above 35, while CAI, CBI, and Fop values ranged from 0.160 to 0.161, −0.078 to −0.076, and 0.362 to 0.363, respectively, indicating a weak preference for codons ending with A/U. Correlation and neutrality analyses suggested that codon usage bias was influenced by both mutation pressure and natural selection, with natural selection being the dominant factor. Fifteen optimal codons, predominantly ending with A/U, were identified. Phylogenetic analysis confirmed the close relationship among the three Medicago species, consistent with traditional taxonomy, whereas the RSCU clustering did not align with the phylogenetic relationships. Conclusions: This study provides insights into the mitochondrial codon usage patterns and their evolutionary determinants in Medicago species, highlighting the predominant role of natural selection in shaping codon usage bias. The findings offer a foundation for comparative genomic studies and evolutionary analyses and may be beneficial for improving genetic engineering and breeding programs of Medicago species. Full article

Background: Grain protein (GPC) and grain starch (GSC) content in common wheat determines suitability for further end-use processing and is an important quality factor. The level of free asparagine in grains (GFAC) significantly affects suitability for thermal processing. The aim of this genome-wide association study (GWAS) was to identify markers associated (MTA) with the levels of GPC, GSC and GFAC in elite winter wheat breeding lines, and to identify candidate genes. Methods: In total, 344 winter wheat lines were phenotyped and genotyped with DArTseq markers. Results: This GWAS revealed 14 MTAs for GPC, 40 for GSC and 43 for GFAC. The new markers were identified and explained from 6.3% to 12.2% of phenotypic variation. For GPC, the region adjacent to marker 4990459 (QGpc.rut.2D) explained 10.2% of the variation and was stable between two years. The novel gene TraesCS7A03G037500, encoding sucrose synthase involved in starch biosynthesis, was identified in the proximity of QGsc.rut.7A.2. The TraesCS1B03G0736700 gene, coding NAD(P)H dehydrogenase subunit H involved in the mitochondrial electron transport chain, was found in the proximity of QGfac.rut.1B.1. Conclusions: These findings provide valuable insights for elucidating inheritance of GCS, and the identified MTAs provide molecular markers for the reduction of free asparagine and increase of protein content in wheat grains. Full article

Background and Objectives: Type 2 diabetes mellitus (T2DM) is a health problem all over the world due to its serious complications such as diabetic nephropathy, diabetic neuropathy, diabetic retinopathy, cardiovascular diseases, and limb amputation. The risk factors for T2DM are environmental, lifestyle, and genetic. The genome-wide association studies (GWASs) have revealed the linkage of certain loci with diabetes mellitus (DM) and its complications. The objective of this study was to examine the association of genetic loci with diabetic nephropathy (DN) in the Saudi population. Materials and Methods: Whole exome sequencing (WES) and bioinformatics analysis, such as Genome Analysis Toolkit, Samtools, SnpEff, Polymorphism Phenotyping v2, and Sorting Intolerant from Tolerant (SIFT), were used to examine the association of gene variations with DN in 26 Saudi patients (18 males and 8 females). Results: The present study showed that there are loci that are probably linked to DM and DN. The genes showed variations that include COCH, PRPF31, PIEZO2, RABL5, CCT5, PLIN3, PDE4A, SH3BP2, GPR108, GPR108, MUC6, CACNA1D, and MAFA. The physiological processes that are potentially affected by these gene variations include insulin signaling and secretion, the inflammatory pathway, and mitochondrial function. Conclusion: The variations in these genes and the dysregulation of these processes may be linked to the development of DM and DN. These findings require further verification in future studies with larger sample sizes and protein functional studies. The results of this study will assist in identifying the genes involved in DM and DN (for example, through genetic counseling) and help in prevention and treatment of individuals or populations at risk of this disease and its complications. Full article

Background: Prunus plants are widely distributed across Asia and Europe, yet their intricate phylogenetic relationships pose significant challenges for systematic studies and interspecies identification. Objectives: To clarify the mitochondrial and chloroplast genomes of Prunus salicina var. cordata, and to reveal its evolutionary relationship and historical gene flow with domesticated cherries. Methods: In this study, we assembled, annotated, and analyzed the first mitochondrial and chloroplast genomes of P. salicina var. cordata, a species within the Prunus genus. Results: The mitochondrial genome was found to be 484,858 base pairs in length, exhibiting a typical circular conformation. Phylogenetic analysis revealed a close evolutionary relationship between P. domestica and P. salicina, suggesting historical gene flow between these two species last genomes; mitochondrial genomes; phylogeny analysis. Conclusions: To provide a genomic basis for resolving the phylogenetic controversies within the Li-associated plants, elucidating their evolutionary mechanisms, and formulating breeding strategies. Full article

Background: Bromus inermis is a high-quality perennial forage grass in the Poaceae family, with significant ecological and economic value. While its chloroplast genome has been sequenced, the mitochondrial genome of this species remains poorly understood due to the inherent complexity and frequent recombination of plant mitochondrial genomes. Methods: We sequenced the complete mitochondrial genome of B. inermis using both Illumina Novaseq6000 and Oxford Nanopore PromethION platforms. Subsequently, comprehensive bioinformatics analyses were performed, including genome assembly and annotation, repetitive sequence identification, codon usage analysis, RNA editing site prediction, the detection of chloroplast-derived sequences, and phylogenetic reconstruction. Results: The mitochondrial genome of B. inermis was determined to be 515,056 bp in length, with a GC content of 44.34%, similar to other Poaceae species. This genome encodes 35 protein-coding genes, 22 tRNA genes, and 10 rRNA genes. Repetitive sequences account for 16.2% of the genome, totaling 83,528 bp, including 124 simple sequence repeats, 293 dispersed repeats, and 31 tandem repeats. A total of 460 RNA editing sites were identified, among which 430 were nonsynonymous. Additionally, 110 putative chloroplast-derived sequences were detected. A phylogenetic analysis based on mitochondrial genome data clarified the species’ evolutionary position within Poaceae. Conclusions: This study provides genetic resources for evolutionary research on and the communication of organelle genomes. Meanwhile, it also lays a solid foundation for the better development and utilization of the germplasm resources of B. inermis. Full article

The objective of this study was to elucidate the proteomic and transcriptomic alterations within the cartilage in Kashin–Beck disease (KBD) compared to a normal control. We conducted a comparison of the expression profiles of proteins, mRNAs, and lncRNAs via data-independent acquisition (DIA) proteomics and transcriptome sequencing in six KBD individuals and six normal individuals. To facilitate the functional annotation enrichment analysis of the differentially expressed (DE) proteins, DE mRNAs, and DE lncRNAs, we employed bioinformatic analysis utilizing Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG). Additionally, we conducted integration analysis of multi-omics datasets using mixOmics. We revealed a distinct proteomic signature, highlighting 53 DE proteins, with notable alterations in the pathways related to tryptophan metabolism and microbial metabolism. Additionally, we identified 160 DE mRNAs, with the functional enrichment analysis uncovering pathways related to RNA metabolism and protein splicing. Furthermore, our analysis of the lncRNAs demonstrated biological processes involved in protein metabolism and cellular nitrogen compound metabolic processes. The integrative analysis uncovered significant correlations, including the positive correlation between superoxide dismutase 1 (SOD1) and mitochondrial import receptor subunit TOM6 homolog (TOMM6), and the negative correlation between C-X9-C motif-containing 1 (CMC1) and succinate–CoA ligase [GDP-forming] subunit beta, mitochondrial (SUCLG2). Our results provide novel insights into the molecular mechanisms underlying KBD. Full article

The Arabian leopard (Panthera pardus nimr), a critically endangered subspecies endemic to the Arabian Peninsula, faces severe threats from habitat loss, prey depletion, and inbreeding, with fewer than 200 individuals remaining. Genomic resources for this subspecies have been scarce, limiting insights into its evolutionary history and conservation needs. Here, we present the first complete mitochondrial DNA (mtDNA) sequence of P. pardus nimr, derived from a wild-born male sampled at the Oman Wildlife Breeding Centre in 2023. Using PacBio HiFi sequencing, we assembled a 16,781 bp mitogenome (GenBank: PQ283265) comprising 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and a control region, with a GC content of 40.94%. Phylogenetic analysis, incorporating 17 Panthera mtDNA sequences, positions P. pardus nimr closest to African leopard populations from South Africa (Panthera pardus), while distinguishing it from Asian subspecies (P. pardus japonensis and P. pardus orientalis). This mitogenome reveals conserved vertebrate mitochondrial structure and provides a critical tool for studying Panthera genus evolution. Moreover, it enhances conservation genetics efforts for P. pardus nimr by enabling population structure analysis and informing breeding strategies to strengthen its survival. Full article

Background/Objectives: Aurochs (Bos primigenius), one of the earliest and largest herbivores domesticated by humans, were widely distributed in Eurasia and North Africa during the Pleistocene and Holocene. Studies of aurochs in China have focused mainly on the Northeastern region. Previous studies have suggested that haplogroup C is a haplogroup unique to China, but recent studies have shown that this is not the case. We have compiled all data on haplogroup C to revisit the classification of the aurochs haplogroup C. Methods: In this study, we obtained 13 nearly complete mitochondrial genomes from Late Pleistocene to early Holocene bovine samples from Northeastern China through fossil sample collection, ancient DNA extraction, library construction, and high-throughput sequencing. Based on the acquired ancient DNA data and in combination with previously published bovine data, the phylogenetic status, lineage divergence time, and population dynamics of aurochs in Northeastern China were analyzed. Results: Phylogenetic analyses and divergence time estimations suggest that the current definition of haplogroup C is overly inclusive, necessitating a refined reclassification of this haplogroup. We also estimated the population dynamics of aurochs in Northeastern China using Bayesian skyline plots found that the maternal effective population size of the aurochs increased significantly during Marine Isotope Stage 5 (MIS5), but began to decrease in the second half of MIS3 before they eventually became extinct. Conclusions: Our results provide new molecular evidence on the phylogenetic status, divergence time, and population dynamics of aurochs in Northeastern China. Full article

Background. The coevolution of nuclear and mitochondrial genomes has guaranteed mitochondrial function for millions of years. The introduction of European (EUR) and African (AFR) genomes into the Ameridian continent during the Columbus exchange in Latin America created an opportunity to naturally test different combinations of nuclear and mitochondrial genomes. However, the impact of potential “mitonuclear discordance” (MND, differences in ancestries) has not been evaluated in Latin American admixed individuals (AMR) affected with developmental disorders, even though MND alters mitochondrial function and reduces viability in other organisms. Methods. To characterize MND in healthy and affected AMR individuals, we used AMR genotype data from the 1000 Genomes Project (n = 385), two cohorts of 22q.11 deletion syndrome patients 22qDS-ARG (n = 26) and 22qDS-CHL (n = 58), and a cohort of patients with multiple congenital anomalies and/or neurodevelopmental disorders (DECIPHERD, n = 170). Based on their importance to mitochondrial function, genes were divided into all mitonuclear genes (n = 1035), high-mt (n = 167), low-mt (n = 793), or OXPHOS (n = 169). We calculated local ancestry using FLARE and estimated MND as the fraction of nuclear mitochondrial genes ancestry not matching the mtDNA ancestry and ∆MND as (MNDoffspring—MNDmother)/MNDmother. Results. Generally, MND showed distinctive population and haplogroup distributions (ANOVA p < 0.05), with haplogroup D showing the lowest MND of 0.49 ± 0.17 (mean ± s.d.). MND was significantly lower in 22qDS-ARG patients at 0.43 ± 0.24 and DECIPHERD patients at 0.56 ± 0.12 compared to healthy individuals at 0.60 ± 0.09 (ANOVA p < 0.05). OXPHOS and high-mt showed the same trend, but with greater differences between healthy and affected individuals. Conclusions. MND seems to inform population history and constraint among affected individuals, especially for OXPHOS and high-mt genes. Full article

Socioeconomic factors have led an increasing number of women to postpone childbirth, thereby elevating the risks of reduced fertility, pregnancy complications, preterm birth, cesarean delivery, and chromosomal abnormalities. While diminished oocyte quality is a well-established contributor to age-related infertility, endometrial dysfunction also plays a pivotal role. Optimizing both oocyte quality and endometrial health is essential for enhancing reproductive outcomes. Although aging has been defined by twelve hallmarks, research specifically addressing age-related changes in endometrial function remains limited. This review examines the process of endometrial aging, with a particular emphasis on mitochondrial function. A comprehensive literature search was conducted using PubMed and Google Scholar to identify relevant studies published up to 31 January 2025. Endometrial aging is driven by multiple biological mechanisms, most notably the decline in endometrial receptivity. Key contributing factors include hormonal dysregulation, chronic inflammation, cell cycle arrest, genomic instability, epigenetic alterations, telomere attrition, and mitochondrial dysfunction. Among these, mitochondrial dysfunction emerges as a central driver of the aging process. Endometrial senescence, precipitated by irreversible mitochondrial impairment, may underlie the progressive decline in reproductive potential. Elucidating the role of mitochondrial dysfunction in aging provides critical insights into the molecular basis of fertility decline, particularly through its impact on endometrial receptivity. Full article