BMC Genomics最新文献

{"title":"The related SNPs and genes to body size using GWAS- latent variable modeling in dromedaries.","authors":"Morteza Bitaraf Sani, Morteza Mokhtari, Zahra Roudbari, Omid Karimi, Nader Asadzadeh, Faisal Almathen, Mohammad Hossein Banabazi","doi":"10.1186/s12864-025-11766-9","DOIUrl":"https://doi.org/10.1186/s12864-025-11766-9","url":null,"abstract":"","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"645"},"PeriodicalIF":3.5,"publicationDate":"2025-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144590427","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":"Genomic functional annotation and comparative analysis of ABC transporter protein family genes in nine types of Chironomidae insects.","authors":"Wenbin Liu, Anmo Zhou, Ziming Shao, Jiaxin Nie, Xinyu Ge, Chuncai Yan, Shaobo Gao, Yiwen Wang","doi":"10.1186/s12864-025-11847-9","DOIUrl":"https://doi.org/10.1186/s12864-025-11847-9","url":null,"abstract":"<p><strong>Background: </strong>The ABC (ATP-binding cassette) transporter family constitutes one of the most extensive transmembrane transporter gene families found across all realms of life. In insects, ABC transporters are crucial for processes such as nutrient metabolism, regulating metamorphosis, and detoxifying xenobiotics. Chironomidae, a diverse aquatic insect group of significant ecological importance that does not bite, has lacked comprehensive annotation of ABC transporters, with the exception of our recent work on Propsilocerus akamusi. In this study, we broaden the annotation by detecting ABC transporter genes across eight additional Chironomidae species, which include all accessible genomes.</p><p><strong>Results: </strong>A total of 454 ABC transporter genes were annotated across the eight species, categorized into eight distinct subfamilies: 67 belonging to the ABCA subfamily, 45 to ABCB, 105 to ABCC, 13 to ABCD, eight to ABCE, 23 to ABCF, 114 to ABCG, and 78 to ABCH. Phylogenetic analysis using Drosophila melanogaster as an external reference revealed clear orthologous relationships for most Chironomidae ABC transporters, except for a notable expansion of the ABCH subfamily.</p><p><strong>Conclusions: </strong>This research offers crucial understanding of the evolutionary processes and physiological roles played by ABC transporters within the Chironomidae species, offering a foundation for understanding their role in the environmental adaptability of these species.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"646"},"PeriodicalIF":3.5,"publicationDate":"2025-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144590426","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 characterization of GRAS gene family and their expression profiles under diverse biotic and abiotic stresses in Amorphophallus konjac.","authors":"Haoliang Shi, Ming Yang, Zhongsi Liu, Jianrong Zhao, Ying Qi, Jianwei Guo, Penghua Gao, Feiyan Huang, Jiani Liu, Lei Yu, Lifang Li","doi":"10.1186/s12864-025-11777-6","DOIUrl":"https://doi.org/10.1186/s12864-025-11777-6","url":null,"abstract":"<p><strong>Background: </strong>The GRAS gene family is a plant-specific group of genes that play critical roles in various biological processes, including plant growth and development, responses to adverse stress, light signaling, hormone signaling, and others. To elucidate the characteristics of the GRAS transcription factor family in Amorphophallus konjac (AkGRAS), we identified GRAS family members based on whole-genome data and bioinformatics methods. We further analyzed their physicochemical properties, gene structure, evolutionary relationships, regulatory networks, and stress response patterns using bioinformatics tools.</p><p><strong>Results: </strong>A total of 57 AkGRAS genes were identified in the A. konjac genome. Most of the encoded proteins were unstable, hydrophilic proteins with molecular weights ranging from 15.78 to 90.82 kDa. Chromosomal localization analysis revealed that the 57 AkGRAS genes were unevenly distributed across 13 chromosomes. Phylogenetic analysis classified the 57 AkGRAS genes into eleven subgroups: DELLA, Os04, SHR, PAT1, HAM, SCR, SCL28, SCL4/7, LAS, LISCL, and SCL3. Six pairs of duplicated genes were identified within the AkGRAS gene family. Protein-protein functional associations analysis suggested that the top three functionally associated proteins were RGA, PAT1-2, and NSP2 in Arabidopsis thaliana. Enrichment analysis predicted the involvement of AkGRAS genes in numerous biological processes. To investigate the expression patterns of AkGRAS genes under Abscisic Acid (ABA), Jasmonic Acid (JA), Salicylic Acid (SA), Pectobacterium carotovorum subsp. carotovorum (Pcc), low temperature, drought, and Salt stresses, we analyzed RNA-seq data and performed RT-qPCR assays. Our results indicated that these genes exhibited tissue-specific expression and diverse responses to biotic and abiotic stresses. Specifically, AkGRAS07, AkGRAS09, and AkGRAS19 expression were upregulated under Pcc infection. AkGRAS19, AkGRAS34, AkGRAS38, and AkGRAS39 were upregulated in response to low-temperature stress. Additionally, AkGRAS09, AkGRAS19, AkGRAS34, and AkGRAS38 were highly induced by drought stress. Notably, AkGRAS23 and AkGRAS53 showed markedly higher expression levels under the 21-day natural drought treatment compared to other conditions. Furthermore, AkGRAS07, AkGRAS09, AkGRAS19, AkGRAS34 and AkGRAS38 were strongly upregulated under 24 h salt treatment.</p><p><strong>Conclusions: </strong>This study identified candidate GRAS genes in A. konjac that may play crucial roles in biotic and abiotic stress responses. The findings provide a theoretical foundation for further research on the functions of AkGRAS genes and their underlying mechanisms in A. konjac stress tolerance.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"643"},"PeriodicalIF":3.5,"publicationDate":"2025-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144590415","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":"Androgen-induced ferroptosis regulates seasonal testicular regression: insights into adaptive mechanisms of seasonal breeding.","authors":"Kang An, Yuchen Tan, Ke Yang, Yukun Kang, Penghui Liu, Biaobiao Hao, Jia Kang, Junhu Su","doi":"10.1186/s12864-025-11770-z","DOIUrl":"https://doi.org/10.1186/s12864-025-11770-z","url":null,"abstract":"","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"644"},"PeriodicalIF":3.5,"publicationDate":"2025-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144590414","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":"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":"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":"&lt;p&gt;&lt;strong&gt;Background: &lt;/strong&gt;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.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Results: &lt;/strong&gt;Ancestry analysis confirmed the admixed nature of the study population, with lower levels of European ancestry significantly associated (p &lt; 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&lt;sup&gt;-8&lt;/sup&gt;, 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&lt;sup&gt;-8&lt;/sup&gt; &lt; p &lt; 10&lt;sup&gt;- 5&lt;/sup&gt;) 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.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Conclusions: &lt;/strong&gt;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":"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":"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":"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":"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":"","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-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}