BMC Genomics最新文献

{"title":"Karyotypic analysis of 62,587 Han Chinese infertile couples undergoing assisted reproductive technology treatments: insights into chromosomal variations.","authors":"Shiheng Zhu, Qian Zhang, Mengchun Hu, Yaxuan Zhang, Anmiao Sun, Xuan Gao, Hong Chen, Junhao Yan","doi":"10.1186/s12864-025-11851-z","DOIUrl":"https://doi.org/10.1186/s12864-025-11851-z","url":null,"abstract":"","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"640"},"PeriodicalIF":3.5,"publicationDate":"2025-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144582995","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Assessing the performance of 28 pathogenicity prediction methods on rare single nucleotide variants in coding regions.","authors":"Jee Yeon Heo, Ju Han Kim","doi":"10.1186/s12864-025-11787-4","DOIUrl":"https://doi.org/10.1186/s12864-025-11787-4","url":null,"abstract":"","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"641"},"PeriodicalIF":3.5,"publicationDate":"2025-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144582993","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Uncovering genetic mechanisms associated with harmful use of alcohol in admixed Latin Americans.","authors":"Edson H B Amaral, Gabriela de S G Britto, Raquel B de São Pedro, Alberto O Moreira, Marília O Scliar, Ricardo Lyra, Natália P Lima, Caroline A Feitosa, Camila A V Figueiredo, Helena M Pitangueira, Thiago Magalhães da Silva, Luydson R S Vasconcelos, Rodrigo F Carmo, Maurício L Barreto, Eduardo Tarazona-Santos, Bernardo L Horta, Ana L Brunialti-Godard, Pablo R S Oliveira","doi":"10.1186/s12864-025-11691-x","DOIUrl":"https://doi.org/10.1186/s12864-025-11691-x","url":null,"abstract":"<p><strong>Background: </strong>Harmful use of alcohol (HUA) refers to drinking patterns that are associated with increased risk of medical complications and adverse social impacts. HUA is a multifactorial condition, involving neurotransmission system alterations, environmental factors, and genetic predisposition. Previous studies have identified numerous genetic variants associated with alcohol-related phenotypes. However, the generalizability of these findings remains limited, as most studies have primarily focused on European and Asian populations, leaving other ethnic groups, such as Latino Americans, underrepresented. Here, we explored the genetic mechanisms underlying HUA in admixed Brazilians. HUA was evaluated in 2,840 individuals using the Alcohol Use Disorder Identification Test (AUDIT). Genetic variations were assessed using a genome-wide genotyping array, followed by genotype imputation. Ancestry patterns were estimated by comparing individual variants with those of reference populations. Association analysis was performed using multivariate logistic regression, and the functional impacts of variants were investigated through in silico analysis. Pathway enrichment and network analyses were conducted to identify potential genetic mechanisms underlying HUA.</p><p><strong>Results: </strong>Ancestry analysis confirmed the admixed nature of the study population, with lower levels of European ancestry significantly associated (p < 0.05, Mann-Whitney U test) with increased risk of HUA, suggesting potential ancestry-related genetic or socio-environmental factors contributing to alcohol-related behaviors. The genome-wide association study identified a significant association between the variant rs1097611 at 1p33 and HUA p = 4.88 × 10<sup>-8</sup>, odds ratio [OR] = 1.8, confidence interval [CI] = 1.46-2.23), based on a multivariate logistic regression model assuming additive genetic effects and adjusted for sex and European ancestry. The rs1097611 and other variants at this locus are located in regulatory regions and have been previously associated with differential CYP4B1 expression across multiple tissues. Other suggestive association signals (5 × 10<sup>-8</sup> < p < 10<sup>- 5</sup>) were identified at loci previously implicated in addictive substance use behaviors, including alcohol and/or tobacco consumption, such as 10q21.2 (ARID5B), 5q34-q35.1 (SLIT3), and 10q11.23 (SGMS1). Genome-based pathway enrichment analysis revealed several mechanisms potentially involved in HUA, primarily related to neurobiological processes and neuronal signaling. Finally, network analysis revealed a highly interconnected cluster of nervous system-related pathways, pointing to their potential functional interplay.</p><p><strong>Conclusions: </strong>This study identifies novel loci, particularly at 1p33 (CYP4B1), and genetic mechanisms potentially involved in HUA in an admixed Latin American population. Studies in diverse ethnic groups are crucial to uncover ","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"639"},"PeriodicalIF":3.5,"publicationDate":"2025-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144582997","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"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":"https://doi.org/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":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome assembly and comparative analysis of Alternaria Linariae reveal novel genes associated with host colonization and virulence.","authors":"Rajan Paudel, Norman Muzhinji, Anju Pandey, Dilip R Panthee, Ralph A Dean, Frank J Louws, Tika B Adhikari","doi":"10.1186/s12864-025-11819-z","DOIUrl":"https://doi.org/10.1186/s12864-025-11819-z","url":null,"abstract":"","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"638"},"PeriodicalIF":3.5,"publicationDate":"2025-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144582994","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","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":"","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":"","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":"","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":"","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":"https://doi.org/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":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}