BMC Genomics最新文献

{"title":"The integration of WGCNA and ceRNA analysis provides insights into bovine intramuscular fat deposition.","authors":"Jiahao Liang, Chenglong Li, Yanfeng Zhang, Yanling Ding, Xiaonan Zhou, Junjie Xu, Xiaowei Wang, Yurun Han, Dingxiang Wang, Yuangang Shi, Yun Ma, Xiaolong Kang","doi":"10.1186/s12864-025-12097-5","DOIUrl":"10.1186/s12864-025-12097-5","url":null,"abstract":"<p><strong>Background: </strong>Intramuscular fat (IMF) content is a crucial determinant of beef quality and a key indicator in cattle breeding and production. However, the molecular regulatory mechanisms governing IMF deposition remain poorly understood.</p><p><strong>Results: </strong>This study preliminarily explored the molecular mechanisms underlying IMF deposition by integrating weighted gene co-expression network analysis (WGCNA) and competitive endogenous RNA (ceRNA) network analysis. Sequencing of longissimus dorsi muscle samples from crossbred Wagyu cattle with varying IMF deposition levels revealed 172 differentially expressed circular RNAs (circRNAs), which were subsequently annotated and used to construct regulatory networks. Protein-protein interaction (PPI) network analysis predicted possible several lipid metabolism-related genes, including EZH2, AKT3, APP and SMARCA5. By combining the miRNA and mRNA data from our previous studies, we constructed circRNA-mRNA coexpression networks and circRNA-miRNA-mRNA regulatory networks. Functional enrichment analysis revealed that the identified circRNAs are involved primarily in lipid metabolism-related pathways, including phosphatidylinositol metabolism and the cGMP-PKG signaling pathway. Additionally, several circRNAs were predicted to function as molecular sponges based on coexpression patterns.</p><p><strong>Conclusion: </strong>This study provides novel insights into the molecular mechanisms underlying IMF deposition in hybrid cattle and provides candidate regulatory mechanisms for further validation in selective breeding.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"865"},"PeriodicalIF":3.7,"publicationDate":"2025-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12482651/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145190790","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":"Genome-wide identification and transcription profiling of safflower (Carthamus tinctorius L.) HD-ZIP gene family under water deficit.","authors":"Fahime Sabzeali, Asadollah Ahmadikhah, Naser Farrokhi, Reza Haghi","doi":"10.1186/s12864-025-12060-4","DOIUrl":"10.1186/s12864-025-12060-4","url":null,"abstract":"","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"874"},"PeriodicalIF":3.7,"publicationDate":"2025-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12482594/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145190795","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":"Investigating the genetic imprint of long body length, high lean meat rate, high fertility and long gestation period in Danish Landrace pigs.","authors":"Jianmei Chen, Ruihua Huang, Jinfeng Ma, Guosheng Su, Min Huang, Wuduo Zhou, Chenxi Liu, Qian Liu, Pinghua Li, Qingbo Zhao","doi":"10.1186/s12864-025-12092-w","DOIUrl":"10.1186/s12864-025-12092-w","url":null,"abstract":"<p><strong>Background: </strong>After long-term artificial selection and lineage mixing, the Danish Landrace pig (DLR), has developed characteristics such as a long body length, high lean meat rate, rapid growth rate, high litter size, and a longer gestation period, with an average gestation length of 117 days. However, the genes responsible for these desirable traits remain partly unknown. According to the breeding history of DLR pigs, it has undergone introgression from British Large White pigs (BLW), selection for high lean meat rate and long body length within the population, and a rapid improvement in reproductive performance since 1992. Research on Danish Duroc and Large White pigs has detected that the lineage of pigs in Taihu Lake region (TL) has introgressed into these two breeds. Therefore, we performed resequencing and chip scanning on 106 TL pigs and 557 DLR pigs, and downloaded 163 resequencing data from Eurasian pigs for shared haplotype analysis, selective sweep analysis, and GWAS.</p><p><strong>Results: </strong>The results indicate that 12 important genes, including CREB3L2, PRKAB2, HIF1A, IGF1, have introgressed from BLW into DLR pigs. These genes enhance lean meat percentage by participating in thermogenesis, oxidative phosphorylation and HIF-1 signaling pathways. In the DLR pig population, 13 shared selected genes were identified across three selective sweep methods. These genes including HBM, RHBDF1, POLR3K, ZNF484, were found to be associated with growth rate, body length, lean meat percentage, and reproductive performance by pheWAS analysis. Interestingly, reproductive performance is primarily related to gestational trait. GWAS for gestational trait in DLR pig population revealed 13 significant genes which also under selection in selective sweeps. These genes include INSYN1, NPTN, NEO1, ZDHHC21. Our study clarifies that the lineage of TL pigs has also introgressed into DLR pigs, with NDUFS4 being an important introgressed gene influencing reproductive performance. Moreover, compared to the low-fertility American Landrace pigs, HTR7, RPP30, ANKRD1, ARHGAP42, and CNTN5 may be important genes selected for enhancing litter size within the DLR pigs.</p><p><strong>Conclusions: </strong>Our research deepens the understanding of the breeding history of DLR pigs, preliminarily identifies genes associated with the characteristics of high lean meat percentage, long body length, and high fertility in DLR pigs, and also finds that the high litter size of DLR pigs may be related to gestation length.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"869"},"PeriodicalIF":3.7,"publicationDate":"2025-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12482165/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145190811","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":"Characteristics of plastid genomes in the Saururaceae and their phylogenomic implications.","authors":"Wei-Hong Sun, Yu Lv, Lian Luo, Ming-Xing Che, Yan Tan, Zhuang Zhao, Tao Feng, Wen-Hui Li, Zhi-Feng Chen","doi":"10.1186/s12864-025-11926-x","DOIUrl":"10.1186/s12864-025-11926-x","url":null,"abstract":"<p><strong>Background: </strong>Saururaceae are an ancient family within Piperales, comprising seven perennial herbs grouped into four relict genera: Anemopsis, Gymnotheca, Houttuynia, and Saururus; distributed primarily in East Asia (Gymnotheca, Houttuynia, and S. chinensis) and North America (Anemopsis and S. cernuus). Despite the limited number of species, phylogenetic relationships remain inconsistent across non-molecular data, nuclear genes, and chloroplast genes.</p><p><strong>Results: </strong>Here, we report for the first time the plastid genomes of G. involucrata and H. emeiensis and provide an additional plastid genome of S. chinensis, enabling a comprehensive analysis of the plastid genome evolution in Saururaceae. All seven plastomes exhibit the typical Quadripartite structure, ranging from 160,226 to 161,556 bp, and contain 131 genes. (114 unique), including 85 protein-coding genes (80 unique), 37 transfer RNAs (tRNAs), eight ribosomal RNAs (rRNAs), and one pseudogene (ycf1). The plastomes are highly conserved in gene order, repeat composition, and codon usage patterns, particularly between H. cordata and H. emeiensis. Mutation hotspots were identified in both coding regions (ycf1, ndhD, ndhF, ccsA, matK; Pi > 0.03) and non-coding regions (rpl32_trnL, rps16_trnQ, ccsA_ndhD, psbM_trnD, psbZ_trnG, ndhE_ndhG, rps15_ycf1, and petA_psbJ; Pi > 0.06), and may serve as molecular markers for species delimitation and population-level studies. Phylogenetic analysis results based on whole plastomes, coding sequences (CDS), and intergenic spacers (IGS) resolve two major clades that correspond to the presence or absence of a flower bract stalk: Anemopsis - Houttuynia (lacking a bract stalk) and Gymnotheca - Saururus (with a bract stalk).</p><p><strong>Conclusion: </strong>This study presents the plastid genomes of G. involucrata and H. emeiensis, revealing structural variations in the plastid genomes of Saururaceae and their implications for internal phylogeny. The findings presented herein provide a novel perspective on the adaptive evolution of Saururaceae, thus offering valuable data for a more in-depth exploration of the phylogeny of Piperales within Magnoliids.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"847"},"PeriodicalIF":3.7,"publicationDate":"2025-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12482058/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145191028","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":"Dissecting alternative splicing patterns of the Rheum palmatum complex with different contents of medicinal constituents.","authors":"Li Yang, Yuxin Fan, Lingli Yang, Tianyi Zhang, Dake Chu, Xumei Wang","doi":"10.1186/s12864-025-12042-6","DOIUrl":"10.1186/s12864-025-12042-6","url":null,"abstract":"","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"855"},"PeriodicalIF":3.7,"publicationDate":"2025-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12482747/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145190697","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":"Genome-wide systematic characterization of PHT gene family and its member involved in phosphate uptake in Orychophragmus violaceus.","authors":"Jianjian Liu, Shuangshuang Wang, Tianyi Ying, Changming Zou, Jianrong Zhao","doi":"10.1186/s12864-025-12091-x","DOIUrl":"10.1186/s12864-025-12091-x","url":null,"abstract":"<p><strong>Background: </strong>Phosphorus (P) is an indispensable mineral element which plays crucial roles in plant development and production. While it is widely acknowledged that phosphate transporters (PHT) facilitate the absorption of P, detailed identification and characterization of the PHT genes in Orychophragmus violaceus remains unexplored.</p><p><strong>Results: </strong>Here, a total of 22 OvPHT genes were identified from high-quality genome of O. violaceus and could be categorized into four distinct subfamilies, based on the phylogenetic analysis. Synteny analysis revealed that the OvPHT gene family underwent nine segmental duplication events and two tandem duplication events. Additionally, a detailed analysis of the Ka/Ks ratios indicated that these duplicated gene pairs primarily experienced purifying selection. Expression patterns of these OvPHT genes across various tissues, including leaves, roots, stems, and flowers, showed differential but partial-overlapping patterns. OvPHT1 members were predominantly expressed in roots and induced by P starvation. Conversely, OvPHT4 members showed high expression levels in all tested tissues, except for roots; the expression levels of OvPHT2 and OvPHT3 members were mainly detected in leaves and flowers, respectively. Moreover, OvPHT1;1 was localized in the plasma membrane. Overexpression of OvPHT1;1 in rice could enhance P uptake under low-P condition.</p><p><strong>Conclusion: </strong>In summary, this systematic analysis provides detailed information for a better understanding of OvPHT genes and identifies candidate genes for further exploration of P-efficient utilization in O. violaceus.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"876"},"PeriodicalIF":3.7,"publicationDate":"2025-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12482593/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145190829","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":"Comprehensive profiling of ribo-seq detected small sequences in yeast reveals robust conservation patterns and their potential mechanisms of origin.","authors":"Cristopher Reyes Loaiciga, Weiyi Li, Xin-Qing Zhao, Jing Li","doi":"10.1186/s12864-025-12064-0","DOIUrl":"10.1186/s12864-025-12064-0","url":null,"abstract":"<p><strong>Background: </strong>In the budding yeast Saccharomyces cerevisiae, the widespread adoption of ribosome profiling technology has allowed the discovery of evidence of transcription and translation for thousands of small proteins or microproteins whose importance was once disregarded. Both conserved and evolutionarily short-lived microproteins have demonstrated relevant involvement in biological functions. However, sequences exist in a broad spectrum of conservation. Here, we tested whether these small proteins in yeast detected by ribosome profiling technology have different properties across their levels of conservation, and how do these properties compare with the canonical small protein-coding sequences.</p><p><strong>Results: </strong>Here, we applied a phylostratigraphic approach to peptides encoded by small open reading frames. We compared 20,023 ribo-seq-detected small peptides against annotated small proteins belonging to reference annotations on the basis of their respective conservation patterns. We identified 1134 unannotated microproteins that, despite their difficulty in being detected by methods other than ribosome profiling, display hallmarks of functionality such as conservation across many taxonomical levels and signals of purifying selection not dissimilar to those of canonical proteins of comparable length. Sequences that initially did not show evidence of belonging to any gene family were found to possess signals of homology traceable mostly at genus level when compared against noncoding regions and using TBLASTN, but also, to a lesser extent, to species belonging to the phyla Basidiomycota and Microsporidia. In addition, we show an analysis of the mutations behind the origin of small open reading frames exclusive to S. cerevisiae and identified changes in the initiation codon as the most common group of mutations when compared to Saccharomyces paradoxus, the closest species to S. cerevisiae.</p><p><strong>Conclusions: </strong>Our work, by presenting robust analysis of the extended landscape of small proteins in yeast, suggests that small conserved sequences, either canonical or not, possess a shared evolutionary trajectory, as demonstrated by their properties. These results shed some light into the evolutionary processes behind the extended landscape of small proteins in yeast.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"856"},"PeriodicalIF":3.7,"publicationDate":"2025-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12482700/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145191074","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":"Aging-TCA: a cross-species single-cell transcriptomic atlas for studying testicular aging.","authors":"Zhihao Lu, Ziyan Zhang, Lingsheng Cao, Gangcai Xie","doi":"10.1186/s12864-025-12090-y","DOIUrl":"10.1186/s12864-025-12090-y","url":null,"abstract":"","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"857"},"PeriodicalIF":3.7,"publicationDate":"2025-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12481971/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145191077","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 MeaB bZIP transcription factor is needed for proper nitrosative stress response induced by nitrite in Aspergillus fumigatus.","authors":"Kinga Edina Varga, Zsigmond Benkő, Károly Antal, Kitti Pázmándi, Zoltán Palczert, István Pócsi, Tamás Emri","doi":"10.1186/s12864-025-11990-3","DOIUrl":"10.1186/s12864-025-11990-3","url":null,"abstract":"<p><strong>Background: </strong>MeaB is a bZIP-type transcription factor in fungi. This protein is known to regulate nitrogen metabolism, contribute to nitrite susceptibility and determine virulence in aspergilli. We hypothesized that MeaB is required for proper nitric oxide (NO) metabolism of fungi. Here, we tested this hypothesis on the human pathogenic fungus Aspergillus fumigatus using a transcriptomics approach.</p><p><strong>Results: </strong>Deletion of the meaB gene increased nitrite, diethylamine NONOate and menadione-sodium bisulfite stress sensitivity, but not that of terc-butyl hydroperoxide or H₂O₂. The conidia of the ΔmeaB mutant showed no altered susceptibility to human macrophages. When the transcriptome of the ΔmeaB strain was compared with the wild-type strain (Af293), genes involved in siderophore biosynthesis or glucanases were enriched in the up-regulated gene set, whereas genes encoding heme-binding proteins or chitinases were enriched in the down-regulated gene set. The 90 mM NaNO₂-induced stress elicited a response in the ΔmeaB gene deletion mutant that was very similar to that of the wild-type strain in the presence of 135 mM NaNO₂. These stress responses included the downregulation of mitotic cell cycle and ribosomal protein genes, and the upregulation of nitrosative stress response (fhpA, fhpB, gnoA), nitrate utilization (niaD, niiA), several iron acquisition and ergosterol biosynthesis genes, as well as the alternative oxidase gene aoxA. These stress treatments also altered the transcriptional activity of secondary metabolite cluster and carbohydrate-active enzyme (CAZyme) genes. Nitrite treatment upregulated arginine metabolism genes only in the wild-type strain. The observed transcriptional changes were associated with reduced growth, increased redox imbalance, increased sterol content in both strains and increased nitrite sensitivity of the ΔmeaB mutant on arginine as sole C and N source.</p><p><strong>Conclusions: </strong>Transcriptomic data implies that MeaB affected fine-tuned regulation of arginine metabolism genes, and the alteration in arginine dependent processes (including siderophore production and possibly NO homeostasis) was responsible for the altered phenotype of the ΔmeaB mutant. Our results also suggest that, although inhibition of A. fumigatus defense against nitrosative stress may not be an effective antifungal therapy for all A. fumigatus strains, a combined approach based on disruption of both iron and NO homeostasis is promising.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"849"},"PeriodicalIF":3.7,"publicationDate":"2025-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12482460/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145190819","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":"Genomic-based revelation of genetic structure and adaptive characterization of Schizopygopsis malacanthus in the Jinsha River and Yalong River.","authors":"Taiming Yan, Kuo Gao, Long He, Yong Pu, Ziting Tang, Jinxin Xiong, Qiqi Chen, Bolin Lai, Fei Liu, Ping Chen, Mingqiang Chen, Wenjie Luo, Junjie Huang, Wenxiang Ding, Deying Yang, Zhi He","doi":"10.1186/s12864-025-12065-z","DOIUrl":"10.1186/s12864-025-12065-z","url":null,"abstract":"","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"870"},"PeriodicalIF":3.7,"publicationDate":"2025-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12482372/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145190791","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}