BMC Genomics最新文献

{"title":"Mechanism of Myh3 gene regulation of intramuscular fat content in Beijing black pigs via the MAPK signaling pathway.","authors":"Yunyan Luo, Gaoxiao Xu, Chunguang Zhang, Zuochen Wen, Han Chu, Yuxing Dai, Liang Hong, Jianbin Zhang, Akpaca Samson Vignon, Chao Sun, Longchao Zhang, Lei Pu","doi":"10.1186/s12864-025-11528-7","DOIUrl":"10.1186/s12864-025-11528-7","url":null,"abstract":"<p><strong>Background: </strong>Intramuscular fat (IMF) content is closely linked to meat tenderness and flavor. The Beijing Black pig, a renowned breed in China, serves as a valuable model for studying IMF traits, with implications for producing high-grade pork.</p><p><strong>Results: </strong>This study identified six single-nucleotide polymorphisms (SNPs) in the myosin heavy chain 3 gene (Myh3) that were significantly associated with IMF traits in Beijing Black pigs. To elucidate the molecular mechanism by which Myh3 affects porcine IMF development, cellular-level studies were conducted. Myh3 interference inhibited the proliferation and differentiation of porcine intramuscular preadipocytes while promoting p38 protein phosphorylation, whereas Myh3 overexpression had the opposite effects. Further investigation using p38 mitogen-activated protein kinase (MAPK) pathway inhibitors and activators revealed that inhibiting the pathway alleviated the suppressive effects of Myh3 interference on differentiation, while activating the pathway reduced the promotive effects of Myh3 overexpression.</p><p><strong>Conclusion: </strong>Our findings demonstrate that Myh3 promotes intramuscular preadipocyte development by inhibiting the p38 MAPK signaling pathway, providing novel insights into the regulatory mechanisms of IMF development.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"642"},"PeriodicalIF":3.5,"publicationDate":"2025-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12236007/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144582996","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 expression analysis of the HvGATA gene family under abiotic stresses in barley (Hordeum vulgare L.).","authors":"Yan Zhao, Chengxin Yin, Ruixi Xing, Jianbin Zeng, Xuehuan Dai, Dengan Xu, Wenxing Liu, Wujun Ma","doi":"10.1186/s12864-025-11834-0","DOIUrl":"10.1186/s12864-025-11834-0","url":null,"abstract":"<p><strong>Background: </strong>GATA transcription factors play crucial roles in plant growth and development, especially in response to environmental stress. Although GATA genes have been studied and identified in various plants, research on these genes in barley is relatively limited.</p><p><strong>Results: </strong>This study identified the GATA gene family and analyzed its gene structure, chromosome distribution, evolutionary analysis, and expression patterns of the HvGATAgene family in barley. The results showed that 27 HvGATA genes are unevenly distributed across seven chromosomes and divided into four subfamilies with similar structures within the same subfamily. Gene synthesis analysis revealed that HvGATA gene family has undergone significant purifying selection. It is noteworthy that the promoter regions of HvGATA genes displayed many cis-acting elements associated with stress responses and hormone regulation. Additionally, the 27 identified genes are predominantly involved in responses to inorganic substances, as indicated by the Gene Ontology (GO) enrichment analysis. The majority of miRNAs that regulate these genes are also capable of modulating abiotic stress responses. Furthermore, expression analysis confirms that the majority of HvGATA genes participate in the regulation of abiotic stresses.</p><p><strong>Conclusion: </strong>In summary, this study contribute to our understanding of important role of HvGATAs in barley, providing a foundation for further exploration of gene function and target genes related to stress responses.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"637"},"PeriodicalIF":3.5,"publicationDate":"2025-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12232774/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144574789","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":"Sex-biased expression of sex-linked transcripts in spiny frogs with homomorphic sex chromosomes.","authors":"Yu Xiao, Yun Xia, Xiaomao Zeng","doi":"10.1186/s12864-025-11846-w","DOIUrl":"10.1186/s12864-025-11846-w","url":null,"abstract":"<p><strong>Background: </strong>The accumulation of sexually antagonistic mutations on chromosomes has been favored in driving the evolution of sex chromosomes. However, empirical evidence has been limited to species with heteromorphic sex chromosomes, where the patterns of gene expression on sex chromosomes differ drastically from those on autosomes. It is little known if the sexualization of gene expression would have started on homomorphic sex chromosomes.</p><p><strong>Results: </strong>To investigate the evolutionary patterns of sex-biased expression, we examined four species of spiny frogs, using high-throughput RNA sequencing for gonads and sex-specific tissues. We find little support for both the enrichment of sex-linked genes and the excess of sex-linked gene expression. Additionally, there is no evidence supporting for sex-biased gene expression near the candidate sex-determining locus. We find no significant accumulation of sex-biased genes on sex chromosomes. Further, the homomorphic sex chromosomes do not show evidence of a faster rate of evolution.</p><p><strong>Conclusions: </strong>The sexualization of sex chromosomes in species with homomorphic sex chromosomes may not be as indispensable as hypothesized.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"636"},"PeriodicalIF":3.5,"publicationDate":"2025-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12229019/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144566967","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 profiling reveals key genes in eggplant (Solanum melongena) roots under salt stress.","authors":"Hongmei Sun, Yong Wang, Lianbin Cao, Yihan Wang, Zhaoyang Wei, Li Song, Jun Jiang, Junhe Liu, Shilin Tian","doi":"10.1186/s12864-025-11802-8","DOIUrl":"10.1186/s12864-025-11802-8","url":null,"abstract":"<p><p>Roots are the initial organs that perceive and adaptively adjust when exposed to salt stress. However, the mechanisms underlying salt stress tolerance in eggplant (Solanum melongena) roots remain elusive. In this study, salt stress markedly elevated the Na⁺ ion concentration, reactive oxygen species (ROS), proline, and malondialdehyde (MDA) content, in addition to enhancing the activities of superoxide dismutase (SOD) and peroxidase (POD) in the roots of the eggplant inbred ZH171. Transcriptome analysis revealed a total of 3491 DEGs in eggplant roots response to salt stress. Most of the DEGs under salt stress were mainly involved in oxidoreductase activity, hydrolase activity, pentose and glucuronate interconversion, microtubule motor activity, ion transport, hydrolytic activity. Some genes were enriched in peroxidase activity, indicating the activation of the antioxidant enzyme system in alleviating oxidative damage under salt stress. A total of 236 DEGs mainly within ERF, MYB, NAC, bHLH, and WRKY TF families, and the most upregulated genes from NAC. Taken together, this study provides important candidate genes linked to salt tolerance in eggplant roots, offering a foundation for further in-depth study of resistance mechanisms in eggplant ZH171.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"635"},"PeriodicalIF":3.5,"publicationDate":"2025-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12228168/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144564254","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 expression pattern of the phytochrome-interacting factors (PIFs) family in three alfalfa varieties.","authors":"Ting Cui, Yong Wang, Kuiju Niu, Huiling Ma","doi":"10.1186/s12864-025-11826-0","DOIUrl":"10.1186/s12864-025-11826-0","url":null,"abstract":"<p><strong>Background: </strong>The Phytochrome-interacting factors (PIFs) are members of the basic helix-loop-helix (bHLH) transcription factor family and play essential roles in plant growth, development, and stress response. While the PIF gene family has been extensively studied in various plant species, there is limited information available regarding their presence in high-quality perennial legume alfalfa (Medicago sativa).</p><p><strong>Results: </strong>In this study, we identified 29, 9, and 27 genes in Xinjiang Daye, Zhongmu No. 1, and Zhongmu No. 4 alfalfa varieties, respectively. These genes are unevenly distributed on 5 chromosomes of Xinjiang Daye, 3 chromosomes of Zhongmu No. 1, and 7 chromosomes of Zhongmu No. 4, with 2 genes not located on any chromosome. Phylogenetic analysis revealed that the MsPIFs genes clustered into five different branches (PIF I to PIF V), with members within the same subfamily sharing conserved motifs and displaying similar exon-intron distribution patterns. Gene duplication analysis indicated that segmental duplications facilitated the expansion and evolution of the alfalfa PIF gene family. Functional cis-element analysis of the MsPIFs genes promoter regions identified elements related to light, hormones, development, and response to abiotic stresses. The expression levels of the majority of MsPIF family genes significantly varied under drought, high temperature, and combined stress conditions, notably showing pronounced responses in genes MsPIF4, MsPIF6, and MsPIF9 to these stressors.</p><p><strong>Conclusion: </strong>We systematically identified and classified the members of the MsPIFs gene family, analyzing their chromosomal locations and genetic structure. These MsPIFs are crucial in alfalfa's responses to drought and high-temperature stress.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"633"},"PeriodicalIF":3.5,"publicationDate":"2025-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12232154/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144558992","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":"Correction: Dissection of genetic basis underlying heat stress response of Apis cerana.","authors":"Ao-Mei Li, Chun-Xiu Pang, Xiao-Lin Cai, Fu-Chang Zhuo, Bo Hu, Xue-Hua Huang, Jia-Xing Huang, Yu-Ming Lu","doi":"10.1186/s12864-025-11837-x","DOIUrl":"10.1186/s12864-025-11837-x","url":null,"abstract":"","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"634"},"PeriodicalIF":3.5,"publicationDate":"2025-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12232131/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144558991","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":"Comparative transcriptomic analysis reveals the important role of hepatic fatty acid metabolism in the acute heat stress response in chickens.","authors":"Zi Mei, Zhenquan Song, Haobo Zhou, Bin Zheng, Yiwei Xiong, Zheya Sheng, Yanzhang Gong","doi":"10.1186/s12864-025-11832-2","DOIUrl":"10.1186/s12864-025-11832-2","url":null,"abstract":"<p><strong>Background: </strong>Heat stress poses a major challenge to global poultry production, but the molecular mechanisms driving the acute heat stress response in multiple organs of chickens remain poorly understood. The present study aimed to elucidate these mechanisms by establishing an acute heat stress chicken model and analyzing the multi-tissue transcriptome and physiological responses.</p><p><strong>Results: </strong>Exposure to 36℃ for 6 h induced marked physiological changes, including elevated rectal temperatures, severe multi-organ damage, and disrupted energy metabolism (increased serum glucose [GLU] and decreased triglycerides [TG] and total cholesterol [TCHO]). Comparative transcriptomic analysis of heart, liver, spleen, lung, and kidney tissues revealed tissue-specific differential gene expression, with the liver and heart showing the highest number of differentially expressed genes (DEGs). KEGG enrichment analyses identified lipid metabolism pathways that are key to the multi-tissue acute heat stress response. Weighted gene co-expression network analysis (WGCNA) further identified 58 differentially modularized hub genes (DMHGs), of which 42 were hepatic differentially expressed genes, and most of these DMHGs were significantly enriched for fatty acid metabolic pathways. Fatty acid metabolic pathway-associated DMHGs were significantly correlated with rectal temperature, serum GLU, TG, lactate dehydrogenase (LDH), and aspartate aminotransferase (AST). Functional validation in primary hepatocytes demonstrated that overexpression of FASN attenuated heat stress-induced reductions in triglyceride levels.</p><p><strong>Conclusions: </strong>The critical role of hepatic fatty acid metabolism in mediating the acute heat stress response in chickens was revealed by a multi-tissue comparative transcriptome, and it was determined that FASN provides actionable insights into improving heat tolerance in poultry through metabolic interventions.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"631"},"PeriodicalIF":3.5,"publicationDate":"2025-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12220621/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144551858","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":"Complete chloroplast genome of two Brachycorythis (Orchidaceae) species from China: comparative analysis and phylogenetic implications.","authors":"Dong Ma, Kaifeng Tao, Yanqiong Xia, Yan Luo, Lu Li","doi":"10.1186/s12864-025-11791-8","DOIUrl":"10.1186/s12864-025-11791-8","url":null,"abstract":"<p><strong>Background: </strong>Brachycorythis Lindl. (Orchidinae, Orchidaceae) was characterized by a large and densely leafy stem throughout its length, comprising about 35 species with African-Asian disjunct distribution. However, the intergeneric and infrageneric phylogeny of Brachycorythis has been debated based on morphological and molecular data. The chloroplast (cp.) genomes of B. henryi and B. menglianensis were investigated in detail and compared with those of related taxa for providing new evidence for the phylogenetics of Brachycorythis.</p><p><strong>Results: </strong>The cp. genomes of B. henryi and B. menglianensis exhibited conserved quadripartite structures, measured 153,006 bp and 152,932 bp in length, with an identical GC content of 37.2%. Gene annotations identified 133 genes, 20 duplicated in the inverted repeat regions. Comparative analysis across their related species confirmed stable sequence identity and higher variation in single-copy regions. Phylogenetic analysis based on complete cp. genomic data revealed that these two Brachycorythis species formed an independent clade exhibiting distinct branch lengths, representing a sister lineage to their related taxa in Orchidinae s. s. It was also supported that six species of Brachycorythis formed a monophyletic clade based on matK + rbcL sequences. Among them, three species from Asia and other three species from Africa, respectively, formed two independent clades. Notably, it was also showed that B. macowaniana was not clustered with other six Brachycorythis species.</p><p><strong>Conclusions: </strong>This is the first report on complete cp. genomic data of Brachycorythis, providing some phylogenetic implications. Some varied cp. genomic features for phylogenetic implications were discussed, including overall genome structure, codon usage, repeat sequences, IR boundaries, DNA polymorphisms, and phylogenetic reconstruction. Based on chloroplast genomic data and matK + rbcL sequence analysis, phylogenetic results revealed that Brachycorythis was not closely related to any of the five genera assumed to be related. Three species from Asia and other three species from Africa, respectively, formed two independent clades, which was consistent well with the African-Asian disjunct distribution of Brachycorythis. And, it was supported that Gyaladenia should be re-established, considering the uncertain species of B. macowaniana. In addition, it was revealed that B. menglianensis was not a synonym of B. henryi, and each of them was a distinct species based on cp. genomic and morphological data. Therefore, the intergeneric and infrageneric relationship of Brachycorythis should be understood better by more cp. genomic data.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"632"},"PeriodicalIF":3.5,"publicationDate":"2025-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12224626/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144551859","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":"Insights to micropsoridia Nosema bombycis congenital infection and host immune responses in the embryo and larva stages of silkworms.","authors":"Tangxin Li, Yue Song, Quan Sun, Qiong Yang, Yunlin Tang, Zigang Shen, Zhangshuai He, Yabin Dou, Junzheng Zhang, Sheng Li, Tian Li, Xianzhi Meng, Zeyang Zhou, Jie Chen, Guoqing Pan","doi":"10.1186/s12864-025-11762-z","DOIUrl":"10.1186/s12864-025-11762-z","url":null,"abstract":"","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"588"},"PeriodicalIF":3.5,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12211725/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144538398","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 multi-omics and biochemical analysis to elucidate the molecular response mechanisms of gill and kidney tissues under acute salinity stress in Pseudobagras ussuriensis.","authors":"Yu Liu, Libo Gu, Jun Zhao, Mengzhu Liu, Ke Wang, Qingbo Zhou, Yang Cao, Ruyi Hu, Weiwei Wang, Qing Liu","doi":"10.1186/s12864-025-11773-w","DOIUrl":"10.1186/s12864-025-11773-w","url":null,"abstract":"","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"590"},"PeriodicalIF":3.5,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12211720/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144538279","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}