BMC Genomics最新文献

{"title":"Identification and evolution of the plant sulfotransferase family.","authors":"Shuangxin Han, Zhujun Chen, Quanlong Liu, Yueying Ding, Jia Wang, Hongbo Liu, Junyang Zou, Zhiying Hong, Hongmei Zhang, Wenping Yang, Lan Zhang, Hongwei Liu, Min Yuan","doi":"10.1186/s12864-025-12117-4","DOIUrl":"10.1186/s12864-025-12117-4","url":null,"abstract":"","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"895"},"PeriodicalIF":3.7,"publicationDate":"2025-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12506393/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145249594","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The two sub-genomes of the allotetraploid frog Xenopus laevis are evolving under similar selective pressure in extant populations.","authors":"Dareen Almojil, Vinu Manikandan, Nizar Drou, John Measey, Stéphane Boissinot","doi":"10.1186/s12864-025-12036-4","DOIUrl":"10.1186/s12864-025-12036-4","url":null,"abstract":"<p><p>The model species Xenopus laevis is an allotetraploid species, whose genome consists of two sub-genomes (the L and S sub-genomes) that were inherited from its parental species. Previous studies comparing the genome of X. laevis with other species of the genus revealed that the L sub-genome was more conserved than the S sub-genome suggesting it has been evolving under stronger purifying selection. However, it remains unclear if this difference reflects evolutionary processes that are still at play in extant populations. To answer this question, we conducted the first genome-wide survey of variation in this species by re-sequencing 44 individuals from its native South African range at ~ 10 × coverage. We generated a dataset of ~ 260M SNPs, which constitutes a valuable resource for the Xenopus community. We found that the South African populations of X. laevis are highly structured and differentiated, reflecting ancient divergence followed by more recent admixture at contact zones. We also determined that the landscapes of variation of the L and S sub-genomes do not show any significant differences suggesting that the two sub-genomes are responding to evolutionary forces in a similar manner. In particular we showed that purifying selection and positive selection are acting identically on the two sub-genomes, suggesting that the sub-genomes of X. laevis are evolving under similar selective pressure. Since 60% of the ancestral homeologous genes have been retained in X. laevis, this result suggests that the function of those genes is conserved on both sub-genomes or that a large number of genes has experienced neo- or sub-functionalization.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"887"},"PeriodicalIF":3.7,"publicationDate":"2025-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12505570/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145243805","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic architecture of the Sindhi Indian population: a 19X-STR forensic analysis.","authors":"Khushboo Gautam, Chanchal Devnani, Shruti Dasgupta, Madhusudan Reddy Nandineni, Kumarasamy Thangaraj, Gyaneshwer Chaubey, Rakesh Rawal","doi":"10.1186/s12864-025-12032-8","DOIUrl":"10.1186/s12864-025-12032-8","url":null,"abstract":"","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"889"},"PeriodicalIF":3.7,"publicationDate":"2025-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12505593/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145243797","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptome analysis of five-toed jerboa organs reveals high-altitude adaptation mechanisms.","authors":"Shan-Shan Sun, Hao-Ting Zhang, Hai-Wen Yan, Xiao-Yu Kang, Qi-Qige Buren, Qian-Cheng Wang, Ming Ming, Jie-Ru Feng, Na Zhu, Xin Li, Yu Ling, Dong Zhang, Xiao-Dong Wu, Shuai Yuan, He-Ping Fu","doi":"10.1186/s12864-025-12096-6","DOIUrl":"10.1186/s12864-025-12096-6","url":null,"abstract":"<p><p>High-altitude environments are characterised by extreme conditions, including hypoxia, low temperatures, and intense ultraviolet radiation. Mammals inhabiting these environments have evolved unique adaptive mechanisms, the study of which elucidates survival strategies and evolutionary pathways under extreme conditions. Understanding how native high-altitude animals respond to such environments is highly important. This study investigated the high-altitude adaptation mechanisms of the five-toed jerboa (Orientallactaga sibirica) distributed in Qinghai Province (4229 m) and Hebei Province (498 m), China, through comparative transcriptomic analysis of heart, lung, and kidney tissues. The results revealed greater mRNA transcriptional differences in the lung tissue than in the heart and kidney tissues of high-altitude jerboas, indicating heightened lung sensitivity to high-altitude conditions. In lung tissue, high-altitude jerboas show differential expression of genes related to the Complement and Coagulation cascades, Heme binding, Oxidation-reduction process (such as MASP1, A2M, SERPING1, CD55, FGA, C5AR1, and KNG1), which may be associated with modulating immune functions to mitigate hypobaric hypoxia, intense radiation, and cold-induced damage and reducing thrombosis and inflammation risks. Heart tissue exhibits differential expression of Oxidative phosphorylation and Lipid metabolism genes (such as NDUFC2, NDUFA3, NDUFS4, COX4I2, PAFAH1B3, SGMS2 and PPAR2B), which may help maintain energy equilibrium under hypoxic and cold challenges. Kidney tissue exhibits differential enrichment of pathways such as arachidonic acid metabolism and steroid hormone biosynthesis mediated by genes including CYP4A11, CYP2C29, GPX2, PTGDS, CBR1, and UGT2B31, which may help coordinate vascular regulation, immune response, and oxidative balance to maintain systemic homeostasis. These pathways and genes are differentially enriched and expressed between high-altitude and low-altitude five-toed jerboas, which may be candidates for further functional studies of plateau environmental adaptability. Our findings provide candidate genes and pathways for intraspecies adaptations across microenvironments and highlight the need for further functional validation.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"888"},"PeriodicalIF":3.7,"publicationDate":"2025-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12506385/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145243760","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Lineage-specific expansions of the Dicer gene family in tardigrades.","authors":"Bethany Weinberg, Teresa W Lee, Natalie C Steinel, Frédéric J J Chain","doi":"10.1186/s12864-025-12050-6","DOIUrl":"10.1186/s12864-025-12050-6","url":null,"abstract":"<p><strong>Background: </strong>RNA interference (RNAi) is an important pathway for gene regulation and immunity. Dicer is a conserved RNAi pathway protein that is found in eukaryotes, with many species expressing multiple dicer gene copies. However, there remains entire lineages such as the phylum Tardigrada with little information about the presence and diversity of dicer genes, limiting our understanding of the evolution and diverse functions of dicer. Our study sought to understand dicer evolution in tardigrades and its phylogenetic relationship to other invertebrate dicers, including the dicer gene duplication in arthropods.</p><p><strong>Results: </strong>Comparative genomic analyses with ten tardigrade species revealed an expansion of dicer genes in tardigrades. The eight Eutardigrades investigated - Hypsibius exemplaris, Ramazzottius varieornatus, Paramacrobiotus metropolitanus, P. fairbanksi, P. richtersi, Richtersius cf. coronifer, Acutuncus antarcticus and Milnesium tardigradum - and two Heterotardigrades Echiniscoides cf. sigismundi and Echiniscus testudo each contain two to four copies of dicer in their genome. Our results are consistent with a Dicer duplication in the common ancestor of Tardigrada and Arthropoda, followed by lineage-specific duplications that form a sister clade to the arthropod Dicer-2. The tardigrade Dicers contain canonical conserved domains including helicase, PAZ, and RNase III, and their domain-specific phylogenetic diversification suggests functional differentiation after duplication, especially for helicase.</p><p><strong>Conclusions: </strong>Our study identified multiple distinct tardigrade-specific dicer duplications following an ancient duplication that is shared in both Eutardigrades and Heterotardigrades. Phylogenetic analyses are consistent with a Dicer duplication before the split of Tardigrada and Arthropoda that led to Dicer-2, which also groups with duplications found in Kinorhyncha and Platyhelminthes. Our study provides insights into Dicer evolution in Tardigrada by characterizing dicer duplications and divergence across various lineages.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"891"},"PeriodicalIF":3.7,"publicationDate":"2025-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12505628/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145243767","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Linkage: an interactive web application for linking of DNA regulatory peaks to genes.","authors":"Siwen Xu, Yuyan Luo, Zenghui Liu, Shaodong Chen, Tianting Li, Chao Zhang, Junxi Zheng, Zixiao Lu, Jin Yang","doi":"10.1186/s12864-025-12115-6","DOIUrl":"10.1186/s12864-025-12115-6","url":null,"abstract":"","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"890"},"PeriodicalIF":3.7,"publicationDate":"2025-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12505793/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145243815","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cell-free DNA-based inference of the activities of 370 + transcription factors mirrors their activities in tumors.","authors":"Ryuji Tamaki, Koji Sagane, Shuyu Dan Li, Taisuke Hoshi","doi":"10.1186/s12864-025-12083-x","DOIUrl":"10.1186/s12864-025-12083-x","url":null,"abstract":"","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"892"},"PeriodicalIF":3.7,"publicationDate":"2025-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12506351/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145243789","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"An R2R3 MYB transcription factor GhMYB5: regulator of CHS expression and proanthocyanin synthesis in brown cotton (Gossypium hirsutum L.).","authors":"Long Chen, Shichang Cheng, Xu Sun, Junshan Gao, Dahui Li, Yujiang Zhang, Ning Guo","doi":"10.1186/s12864-025-12053-3","DOIUrl":"10.1186/s12864-025-12053-3","url":null,"abstract":"<p><strong>Background: </strong>Cotton (Gossypium spp.) serves as a vital global crop for textile production, with naturally pigmented brown cotton has gained industrial interest due to its eco-friendly coloration. However, the molecular mechanisms underlying variation in color intensity in brown cotton fibers remain poorly characterized. In this study, we investigated the genetic and biochemical basis of fiber color differentiation in hybrid-derived cotton lines spanning white, light-brown, middle-brown, and deep-brown phenotypes.</p><p><strong>Results: </strong>Biochemical quantification revealed significantly elevated proanthocyanidin levels in brown cotton fibers compared to those in white counterparts, with their content positively correlating with color intensity. Transcriptomic profiling identified significant activation of flavonoid biosynthesis pathway genes in pigmented fibers. Among differentially expressed transcription factors, GhMYB5 (Ghir_D07G002110), an R2R3-type MYB regulator, exhibited gradual upregulation corresponding to color deepening. Functional characterization through qRT-PCR demonstrated GhMYB5's potential regulation of key flavonoid pathway genes GhCHS1 (Ghir_A10G012390), GhCHI3 (Ghir_A05G041560), and GhF3H (Ghir_D11G018670). Protein-DNA interaction assays (DAP-seq), yeast one-hybrid validation and LUC analysis confirmed direct binding of GhMYB5 to the promoter region of GhCHS1, establishing a regulatory node in proanthocyanidin biosynthesis.</p><p><strong>Conclusions: </strong>Our findings reveal that GhMYB5-mediated transcriptional activation of GhCHS1 promotes proanthocyanidin accumulation in brown cotton fibers, providing a molecular explanation for color intensification. The identified MYB-CHS regulatory module offers potential targets for molecular breeding of naturally colored cotton varieties with enhanced pigmentation properties. This study advances our understanding of plant pigment biosynthesis and supports sustainable textile production through engineering of natural fiber coloration.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"884"},"PeriodicalIF":3.7,"publicationDate":"2025-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12502274/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145237921","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Integrative analysis of Hub1 overexpression: driving transcriptional reprogramming and alternative splicing in Saccharomyces cerevisiae.","authors":"N M Asif Billah, Umama Khan, Kazi Mohammed Didarul Islam, S M Abdul-Awal, Md Morsaline Billah","doi":"10.1186/s12864-025-12006-w","DOIUrl":"10.1186/s12864-025-12006-w","url":null,"abstract":"<p><strong>Background: </strong>Hub1, a conserved ubiquitin-like protein, is essential for pre-mRNA splicing and transcriptional regulation in Saccharomyces cerevisiae. Despite its known functions, the genome-wide effects of Hub1 overexpression remain largely uncharacterized. This study investigates the transcriptomic and splicing landscape changes triggered by Hub1 overexpression using an integrative bioinformatic approach.</p><p><strong>Results: </strong>We analyzed RNA-seq data from the GSE84215 dataset, employing differential expression, alternative splicing, functional enrichment, and network-based methods. DESeq2 identified 3,915 differentially expressed genes (DEGs; 1,964 upregulated, 1,951 downregulated, padj < 0.05), demonstrating extensive transcriptional reprogramming. Principal component analysis revealed that Hub1 overexpression explained 98% of transcriptional variance, indicating its dominant regulatory influence. Using rMATS, we detected seven exon skipping events, with DYN2 showing significant differential splicing (FDR = 0.0481, ΔPSI = - 0.036). MaxEntScan analysis confirmed that DYN2's 5' splice site is significantly weaker than canonical yeast splice sites (score = - 18.32, p = 0.03), consistent with Hub1's role in facilitating non-consensus splicing. Functional enrichment analyses revealed metabolic reprogramming, with upregulated pathways including biosynthesis of secondary metabolites and carbon metabolism, while growth-related processes like ribosome biogenesis and cell cycle were downregulated. Gene Set Enrichment Analysis (GSEA) further supported stress response activation (p53 signaling, NES = 1.255) and cell cycle suppression (NES = - 0.692). Weighted Gene Co-expression Network Analysis (WGCNA) identified 61 co-expression modules, with the brown module highly correlated with Hub1 overexpression (r = 0.99, p < 0.001) and enriched in biosynthetic and proteasome pathways. Protein-protein interaction network analysis revealed 35 Hub1 interactors, including spliceosomal components, reinforcing its central role in RNA processing.</p><p><strong>Conclusion: </strong>Our findings reveal that Hub1 overexpression drives coordinated transcriptional and post-transcriptional changes, promoting metabolic reprogramming while specifically modulating splicing of genes with weak splice sites like DYN2. These results establish Hub1 as a dual regulator linking transcriptional control with splicing precision, suggesting a regulatory mechanism that enhances cellular adaptability under stress conditions.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"885"},"PeriodicalIF":3.7,"publicationDate":"2025-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12502333/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145237600","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of novel RNA polymerase III promoters in bovine leukemia virus miRNA cluster by cross-taxa analysis of small non-coding RNAs.","authors":"Aneta Pluta, Casey Droscha","doi":"10.1186/s12864-025-12074-y","DOIUrl":"10.1186/s12864-025-12074-y","url":null,"abstract":"<p><strong>Background: </strong>Bovine leukemia virus (BLV) is an oncogenic deltaretrovirus that induces enzootic bovine leukosis. A defining feature of BLV is its viral miRNA cluster, which is transcribed atypically by RNA polymerase III via internal type 2 promoters rather than through the canonical Pol II pathway. These miRNAs accumulate to high levels within infected lymphocytes and can alter expression of a variety of host genes involved in lymphocyte proliferation and impose leukemogenic processes.</p><p><strong>Results: </strong>Here, we present a comprehensive in silico characterization of new A-box and B-box promoter motifs within the BLV miRNA-coding region. As the first step, a taxonomically diverse dataset of small non-coding RNAs (tRNAs, SINEs, and other ncRNAs) was assembled to derive position-weight matrices and corresponding IUPAC consensus sequences for type 2 internal Pol III promoter motifs. Using these models, all available BLV miRNA cluster sequences were scanned to identify and map A-box-like and B-box-like elements and to reconstruct the underlying promoter architecture. Our analyses reveal a noncanonical BLV promoter organization: overlapping degenerate A-box variants-most frequently three distinct elements-reside within the pre-miRNA hairpin region, whereas B-box elements were positioned downstream of the Pol III termination signal, effectively excluded from the mature transcript.</p><p><strong>Conclusions: </strong>Despite motif degeneration, critical nucleotide positions remained strongly conserved, indicating evolutionary pressure to preserve Pol III recruitment while accommodating viral genome constraints. These findings fill a crucial gap in understanding of BLV Pol III promoter architecture and provide a foundation for future studies on how unconventional promoter configurations regulate viral miRNA expression and virus-host interactions.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"882"},"PeriodicalIF":3.7,"publicationDate":"2025-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12498455/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145237899","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}