BMC Genomics最新文献

{"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}

{"title":"Differential detection workflows for multi-sample single-cell RNA-seq data.","authors":"Jeroen Gilis, Laura Perin, Milan Malfait, Helena L Crowell, Koen Van den Berge, Alemu Takele Assefa, Bie Verbist, Davide Risso, Lieven Clement","doi":"10.1186/s12864-025-12102-x","DOIUrl":"10.1186/s12864-025-12102-x","url":null,"abstract":"<p><p>In single-cell transcriptomics, differential expression (DE) tools compare average expression between cell types or conditions. However, scRNA-seq technologies hold the promise to infer differences in other aspects of the expression distribution. We therefore developed workflows for differential detection (DD) to infer differences in the average fraction of cells in which expression is detected. After benchmarking eight DD strategies, we present a unified workflow for jointly assessing DE and DD. Through simulations and two case studies, we demonstrate that our joint analyses provide complementary information, both in terms of the individual genes they report and in their functional interpretation.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"886"},"PeriodicalIF":3.7,"publicationDate":"2025-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12502395/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145237906","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":"Computational investigation of the sequence context of arginine/glycine-rich motifs in the human proteome.","authors":"Eric Schumbera, Dorothee Dormann, Andreas Walther, Miguel A Andrade-Navarro","doi":"10.1186/s12864-025-12132-5","DOIUrl":"10.1186/s12864-025-12132-5","url":null,"abstract":"<p><p>Arginine-glycine (RG)-rich motifs are among the most prevalent RNA-binding elements within intrinsically disordered regions (IDRs) of proteins and play crucial roles in RNA metabolism, gene regulation, and the formation of membraneless organelles via liquid phase separation (LLPS). Despite their biological relevance and implication in neurological disorders and cancer, the sequence features and context dependencies that define functional RG motifs remain poorly characterized owing to their disordered nature and sequence variability. In this study, we present a computational framework to dissect the sequence and structural context of RG motifs across the human proteome. By contrasting a functionally defined positive dataset-enriched for RNA-binding and phase-separating proteins-with a negative dataset of RG motif proteins lacking these annotations, we identified distinct compositional and contextual signatures. RG motifs in the functionally defined positive dataset show increased enrichment of phenylalanine, tyrosine, aspartic acid, and asparagine, both within and around the motif, as well as nonrandom spatial relationships with structured RNA-binding domains. Notably, phenylalanine and tyrosine exhibit divergent positional and functional profiles, suggesting distinct mechanistic roles. Our analysis highlights the potential of sequence-based approaches to uncover functional determinants in disordered protein regions and further advances our understanding of the properties of RG motifs, offering a transferable framework for the study of other low-complexity motifs.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"883"},"PeriodicalIF":3.7,"publicationDate":"2025-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12502372/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145237891","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":"Large-scale genome sequencing reveals population separation and selection signatures in major canyon yaks.","authors":"Zemin Li, Jiahong Zhao, Xingyu Guo, Shiyu Wu, Shikai Wang, Jincheng Zhong, Yixi Kangzhu, Jikun Wang, Daoliang Lan, Jiabo Wang","doi":"10.1186/s12864-025-12114-7","DOIUrl":"10.1186/s12864-025-12114-7","url":null,"abstract":"<p><p>Through long-term natural and artificial selection, domestic yaks (Bos grunniens) have diverged from wild ancestors and become vital to high-altitude pastoralism, providing meat, milk, fiber, and other essential resources and transportation. Especially, based on the complex and changeable environments in the canyon of the Tibetan Plateau, the canyon-type yaks show diverse phenotypic traits, including morphology, production, and adaptation. To explore the genetic basis of this breed-specific adaptation and identify key functional genes shaped by selection, we collected 225 yaks from three canyon-type yak populations and scanned genome variation information using high-throughput resequencing. We employed three approaches, nucleotide diversity (π), fixation index (Fst) and cross-population extended haplotype homozygosity (XPEHH), to detect positive selection signals in the genome. Through analyses of population structure, genetic diversity, and selection sweep signals, we identified unique Single Nucleotide Polymorphisms (SNPs) that reveal significant genomic divergence among the three yak populations, which can also serve as genetic markers for population discrimination. Furthermore, shared SNPs identified by selective sweep analysis exhibited distinctive Minor Allele Frequency (MAF) distribution patterns; these population-specific SNP markers can be directly applied to develop SNP chips for breed-specific identification. A total of 13 genes related to breed-specific adaptive traits were identified. These findings provide valuable insights into the molecular signatures of breed-specific adaptation under human management and natural selection. It also identifies key functional genes relevant to future breeding programs.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"881"},"PeriodicalIF":3.7,"publicationDate":"2025-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12495853/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145224703","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":"Exploring the genetic basis of heterosis in eucalypt growth based on transcriptome analysis.","authors":"Zhiyi Su, Wanhong Lu, Yan Lin, Guo Liu, Anying Huang, Jianzhong Luo","doi":"10.1186/s12864-025-12077-9","DOIUrl":"10.1186/s12864-025-12077-9","url":null,"abstract":"","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"880"},"PeriodicalIF":3.7,"publicationDate":"2025-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12492705/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145224684","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}