BMC Genomics最新文献

{"title":"CanASM: a comprehensive database for genome-wide allele-specific DNA methylation identification and annotation in cancer.","authors":"Jianmei Zhao, Zeyu Zhao, Hongfei Li, Haojie Yu, Hao Lin, Hanqi Chen, Xuecang Li, Di Liu, Yiming Wang, Guohua Wang","doi":"10.1186/s12864-025-11849-7","DOIUrl":"https://doi.org/10.1186/s12864-025-11849-7","url":null,"abstract":"<p><p>Allele-specific DNA methylation (ASM) provides critical insights into the complex genetic and epigenetic mechanisms regulating gene transcription. Emerging evidence suggests that ASM is particularly enriched in gene enhancer regions, and recent studies have demonstrated that ASM is increased in cancer tissues compared with normal tissues. Despite the increasing recognition of ASM as a potential biomarker in tumorigenesis, systematic resources dedicated to identifying and annotating ASMs in cancer contexts remain limited. In this study, we developed CanASM ( https://bioinfor.nefu.edu.cn/CanASM/ ), the first comprehensive database specifically designed to identify and annotate ASM in cancer. In CanASM, ASM sites identified from bisulfite sequencing (BS-Seq) data across 31 cancer types and their matched normal tissue samples are cataloged. Importantly, CanASM includes extensive regulatory annotations for ASMs, including associated genes, cis-regulatory elements and transcription factor binding colocalizations, transcription factor affinity changes, etc. Users can query and explore ASMs using various parameters, such as single-nucleotide variations (SNVs), chromosomal coordinates, and gene names. The current version of CanASM includes 5,003,877 unique SNV-CpG pairs, including 3,056,776 index SNVs, of which 2,634,406 are single-nucleotide polymorphisms (SNPs), and 4,157,508 CpGs. With an intuitive interface for browsing, querying, analyzing, and downloading, CanASM serves as a valuable resource for researchers investigating cancer-associated genetic variations and epigenetic regulation in cancer.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"648"},"PeriodicalIF":3.5,"publicationDate":"2025-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144599319","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":"Comparative genomic and functional analyses of Microbacterium paraoxydans BHS25 reveal key metabolic adaptations for survival in arsenic-contaminated soil ecosystems.","authors":"Ayman Bin Abdul Mannan, Momtaz Zamila Bukharid, M Anwar Hossain, Munawar Sultana","doi":"10.1186/s12864-025-11811-7","DOIUrl":"https://doi.org/10.1186/s12864-025-11811-7","url":null,"abstract":"<p><strong>Background: </strong>Microbacterium paraoxydans is known for its potential in bioremediation and biotechnological applications, including promoting plant growth. However, research on this bacterium in Bangladesh has been limited and until now no reported complete genome of M. paraoxydans is available from this country. In this study, we have reported the complete genome of M. paraoxydans BHS25, the first case in Bangladesh, isolated from arsenic-contaminated soil in Bogura.</p><p><strong>Results: </strong>Complete genome analysis revealed that BHS25 was closely related to Microbacterium paraoxydans LTR1 from Russia, which itself showed similarity to a strain found at the International Space Station, reported to be resistant to extreme conditions. BHS25 possessed a genome of 3.49 Mb with a GC content of 70.12%, comprising 3,415 protein-coding genes, 47 tRNA genes, and 5 rRNA genes. It carried various heavy metal resistance genes and gene islands, such as arsC, arsB, and acr3 for arsenic detoxification/transformation, as well as czcD and copB for resistance to cadmium, zinc, cobalt, and copper. The arrangement of the arsenic resistance genes showed similarity to that in other reported Microbacterium strains, although pangenome and ANI analyses indicated considerable genetic diversity within the species. Additionally, the presence of vanY within the vanB cluster suggested potential vancomycin resistance. Metabolic pathway analyses revealed that BHS25 was well adapted, with different carbohydrate and amino acid metabolism, secondary metabolite biosynthesis, and xenobiotic degradation capabilities. The unique notable anabolic pathways were streptomycin biosynthesis with 14 associated genes, novobiocin biosynthesis and tropane, piperidine, and pyridine alkaloid biosynthesis (8 genes each), as well as monobactam biosynthesis, prodigiosin biosynthesis, and penicillin and cephalosporin biosynthesis, suggesting a potential for production of antimicrobials. Furthermore, it showed an auxin biosynthesis pathway for plant growth, further demonstrating its biotechnological potential.</p><p><strong>Conclusion: </strong>This research identified Microbacterium paraoxydans BHS25 as a promising candidate for bioremediation and sustainable environmental management, offering insights into microbial adaptation to challenging environments and potential solutions for pollution encounters.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"650"},"PeriodicalIF":3.5,"publicationDate":"2025-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144599320","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":"Molecular mechanisms underlying leaf enlargement in spaceflight-mutated 'Deqin'alfalfa.","authors":"Qian Kuang, Rui Ding, Die Huang, Chenggang He, Hua Jiang","doi":"10.1186/s12864-025-11845-x","DOIUrl":"https://doi.org/10.1186/s12864-025-11845-x","url":null,"abstract":"","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"649"},"PeriodicalIF":3.5,"publicationDate":"2025-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144599321","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":"Whole-transcriptome sequencing reveals the global molecular responses and ceRNA regulatory network involved in programmed cell death of rice cultivars zyk639 and zyk-lm.","authors":"Haipeng Zhang, Han Zheng, Weifang Liang, Junjie Zhang, Hongyu Zhao, Jianzhong Li, Yujie Zhou, Liujie Xie, Chulang Yu, Binfeng Dai, Liequan Zhong, Fan Hou, Chengyu Wang, Jianping Chen, Yong Yang","doi":"10.1186/s12864-025-11844-y","DOIUrl":"https://doi.org/10.1186/s12864-025-11844-y","url":null,"abstract":"<p><strong>Background: </strong>Programmed cell death (PCD) can be triggered by biotic stress or abiotic stress in rice, which is a crucial factor throughout the lifecycle. Long non-coding RNAs (lncRNAs) have important roles in a variety of biological processes. However, the regulatory relationship between lncRNAs and rice PCD occurrence is unclear.</p><p><strong>Methods: </strong>In this study, messenger RNAs (mRNAs) and lncRNAs associated with PCD regulation were identified in two rice cultivars: japonica rice (Oryza sativa) cultivar zheyoukang639 (zyk639) and its mutant zyk639-lesion mimic (zyk-lm). Besides, these data were used for weighted gene co-expression analysis (WGCNA) and construction of competitive endogenous RNAs (ceRNAs).</p><p><strong>Results: </strong>As a result, 5,289 lncRNAs and 39,475 mRNAs were identified, of which 1,873 lncRNAs and 11,930 mRNAs were differentially expressed. In addition, WGCNA showed that the blue module was critical for the development of PCD in rice. The construction of the ceRNA regulatory network associated with the occurrence of PCD in rice identified 101 pairs of relationships, including 9 lncRNAs, 11 miRNAs and 76 mRNAs. Importantly, three major lncRNAs in zyk-lm, including MSTRG.24301.2, MSTRG.17476.1 and MSTRG.24898.1, may be involved in leaf PCD, with MSTRG.24898.1 binding to osa-miR580 to regulate transcription factors. Furthermore, the lncRNAs co-expression mRNAs rpl27-1 and OsRPS27, which were associated with ribosomal genesis, and Os11g0490900, a WRKY family transcription factor, may also regulate PCD genesis.</p><p><strong>Conclusions: </strong>Models of protein synthesis regulation associated with zyk-lm PCD were discussed, lncRNAs may serve as key factors in regulating PCD and provide ideas for understanding PCD and genetic messaging.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"647"},"PeriodicalIF":3.5,"publicationDate":"2025-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144599322","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":"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":"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":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12232865/pdf/","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":"OA","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":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12235850/pdf/","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":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}