BMC Genomics最新文献

{"title":"A comprehensive catalog of single nucleotide polymorphisms (SNPs) from the black pepper (Piper nigrum L.) genome.","authors":"Hiruni A Thanthirige, Nilni A Wimalarathna, Anushka M Wickramasuriya","doi":"10.1186/s12864-025-11414-2","DOIUrl":"https://doi.org/10.1186/s12864-025-11414-2","url":null,"abstract":"<p><strong>Background: </strong>Single nucleotide polymorphisms (SNPs) have emerged as the marker of choice in breeding and genetics, particularly in non-model organisms such as black pepper (Piper nigrum L.), a globally recognized spice crop. This study presents a comprehensive catalog of SNPs in the black pepper genome using data from 30 samples obtained from RNA sequencing and restriction site-associated DNA sequencing, retrieved from the Sequence Read Archive, and their consequences at the sequence level.</p><p><strong>Results: </strong>Three SNP calling and filtering pipelines, namely BCFtools, Genome Analysis Toolkit (GATK)-soft filtering, and GATK-hard filtering, were employed. Results revealed 498,128, 396,003, and 312,153 SNPs respectively identified by these pipelines, with 260,026 SNPs commonly detected across all methods. Analysis of SNP distribution across the 45 scaffolds of the black pepper genome showed varying densities, with pseudo-chromosomes Pn25 (0.86 SNPs/kb), Pn8 (0.74 SNPs/kb), and Pn7 (0.72 SNPs/kb) exhibiting the highest densities. Conversely, scaffolds Pn27 to Pn43 exhibited minimal SNP distribution, except Pn45. Approximately 34.80% of SNPs exhibited stronger genetic linkage (r² > 0.7). Moreover, SNPs predominately mapped to downstream (≈ 32.54%), upstream (≈ 22.52%), and exonic (≈ 16.20%) regions of genes. Transition substitution accounted for the majority (≈ 57.42%) of identified SNPs, resulting in an average transition-to-transversion ratio of 1.36. Notably, 56.09% of SNPs were non-synonymous, with a significant proportion (≈ 53.59%) being missense mutations. Additionally, 12,491 SNPs with high or moderate impacts were identified, particularly in genes associated with secondary metabolism and alkaloid biosynthesis pathways. Furthermore, the expression of 675 genes was potentially influenced by local (cis-acting) SNPs, while 554 genes were affected by distal (trans-acting) SNPs.</p><p><strong>Conclusion: </strong>The findings of the present study underscore the utility of identified SNPs and their targets, especially those impacting important pathways, for future genetic investigations and crop improvement efforts in black pepper. The characterization of SNPs in genes related to secondary metabolism and alkaloid biosynthesis highlights their potential for targeted breeding aimed at enhancing the yield, quality, and resilience of this economically important crop in diverse environmental conditions.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"256"},"PeriodicalIF":3.5,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143647185","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":"SLAF-seq technology-based genome-wide association and population structure analyses of hot pepper and sweet pepper.","authors":"Yaning Meng, Hongxiao Zhang, Zhe Zhang, Xinxin Li, Zhanghong Yu, Yanqin Fan, Libin Yan","doi":"10.1186/s12864-025-11454-8","DOIUrl":"https://doi.org/10.1186/s12864-025-11454-8","url":null,"abstract":"<p><strong>Background: </strong>Utilizing Single Nucleotide Polymorphism (SNP) marker technology, a phylogenetic and agronomic trait network analysis was conducted on the collected hot pepper and sweet pepper germplasm resources, providing a theoretical basis for parental selection and new varieties.</p><p><strong>Results: </strong>Specific-locus amplified fragment sequencing (SLAF-seq) technology was employed for a genome-wide association study (GWAS) on 197 hot pepper and sweet pepper germplasm resources, generating 1404.88 Mb clean reads data with an average Q30 of 91.5% and mean GC content of 37.96%. Through sequencing data analysis, a total of 639,815 SLAF tags were obtained with an average sequencing depth of 12.16x, among which 86,381 were polymorphic SLAF tags, leading to the development of 18,145,155 SNP markers. The identified SNP markers were used for cluster analysis of the genetic structure and phylogenetic relationships of hot pepper and sweet pepper germplasm resources, dividing the 197 hot pepper and sweet pepper germplasm resources into 9 clusters. Additionally, a genome-wide association analysis was conducted on 25 agronomic traits of the 197 hot pepper and sweet pepper materials, yielding a substantial number of significantly associated SNP loci with agronomic traits. A correlation network analysis diagram was drawn among the various agronomic traits, preliminarily determining the relationships between the 25 agronomic characteristics of hot pepper and sweet pepper and the positions of 15 agronomic traits (p < 1.707 × 10^-8) on the chromosomes were annotated, forming multi-trait aggregation regions.</p><p><strong>Conclusions: </strong>Our research reveals the genetic diversity, phylogenetic relationships, and population structure of 197 hot pepper and sweet pepper germplasm resources, providing a basis for germplasm identification, resource utilization, and breeding.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"258"},"PeriodicalIF":3.5,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143647186","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: Advancing genetic improvement in the omics era: status and priorities for United States aquaculture.","authors":"Linnea K Andersen, Neil F Thompson, Jason W Abernathy, Ridwan O Ahmed, Ali Ali, Rafet Al-Tobasei, Benjamin H Beck, Bernarda Calla, Thomas A Delomas, Rex A Dunham, Christine G Elsik, S Adam Fuller, Julio C García, Mackenzie R Gavery, Christopher M Hollenbeck, Kevin M Johnson, Emily Kunselman, Erin L Legacki, Sixin Liu, Zhanjiang Liu, Brittany Martin, Joseph L Matt, Samuel A May, Caitlin E Older, Ken Overturf, Yniv Palti, Eric J Peatman, Brian C Peterson, Michael P Phelps, Louis V Plough, Mark P Polinski, Dina A Proestou, Catherine M Purcell, Sylvie M A Quiniou, Guglielmo Raymo, Caird E Rexroad, Kenneth L Riley, Steven B Roberts, Luke A Roy, Mohamed Salem, Kelly Simpson, Geofrey C Waldbieser, Hanping Wang, Charles D Waters, Benjamin J Reading","doi":"10.1186/s12864-025-11447-7","DOIUrl":"10.1186/s12864-025-11447-7","url":null,"abstract":"","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"260"},"PeriodicalIF":3.5,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143647166","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":"Chromosome-level genome assembly of Eimeria tenella at the single-oocyst level.","authors":"Kaihui Zhang, Yudong Cai, Yuancai Chen, Yin Fu, Ziqi Zhu, Jianying Huang, Huikai Qin, Qimeng Yang, Xinmei Li, Yayun Wu, Xun Suo, Yu Jiang, Longxian Zhang","doi":"10.1186/s12864-025-11423-1","DOIUrl":"https://doi.org/10.1186/s12864-025-11423-1","url":null,"abstract":"<p><strong>Background: </strong>Eimeria are obligate protozoan parasites, and more than 1,500 species have been reported. However, Eimeria genomes lag behind many other eukaryotes since obtaining many oocysts is difficult due to a lack of sustainable in vitro culture, highly repetitive sequences, and mixed species infections. To address this challenge, we used whole-genome amplification of a single oocyst followed by long-read sequencing and obtained a chromosome-level genome of Eimeria tenella.</p><p><strong>Results: </strong>The assembled genome was 52.13 Mb long, encompassing 15 chromosomes and 46.94% repeat sequences. In total, 7,296 protein-coding genes were predicted, exhibiting high completeness, with 92.00% single-copy BUSCO genes. To the best of our knowledge, this is the first chromosome-level assembly of E. tenella using a combination of single-oocyst whole-genome amplification and long-read sequencing. Comparative genomic and transcriptome analyses confirmed evolutionary relationship and supported estimates of divergence time of apicomplexan parasites and identified AP2 and Myb gene families that may play indispensable roles in regulating the growth and development of E. tenella.</p><p><strong>Conclusion: </strong>This high-quality genome assembly and the established sequencing strategy provide valuable community resources for comparative genomic and evolutionary analyses of the Eimeria clade. Additionally, our study also provides a valuable resource for exploring the roles of AP2 and Myb transcription factor genes in regulating the development of Eimeria parasites.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"257"},"PeriodicalIF":3.5,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143647199","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 transcriptome analysis reveals differences in immune responses to copper ions in Sepia esculenta under high-temperature conditions.","authors":"Yancheng Zhao, Deyuan Chang, Yanxuan Zheng, Yuwei Zhang, Yongjie Wang, Xiaokai Bao, Guohua Sun, Yanwei Feng, Zan Li, Xiumei Liu, Jianmin Yang","doi":"10.1186/s12864-025-11418-y","DOIUrl":"10.1186/s12864-025-11418-y","url":null,"abstract":"<p><p>Sepia esculenta is one of the most abundant extant squid populations in Southeast Asia and is of interest due to its rapid reproductive rate and high commercial value. In recent years, with the rapid development of industrialization, issues such as global warming and heavy metal pollution in the oceans have emerged, posing a serious threat to the life activities of marine organisms. In this study, we used transcriptomic techniques to investigate the differences in Cu exposure immune responses in S. esculenta larvae under different temperature conditions. The enrichment of solute carrier family (SLC) genes and genes related to DNA replication and damage was significantly higher in the CuT group than in the Cu group. Functional enrichment analysis revealed that the FcγR-mediated phagocytosis and autophagy pathways were enriched in the CuT group. Based on the analysis of differentially expressed genes (DEGs) and functional enrichment results, we can preliminarily infer that the CuT group caused more severe disruption of intercellular ion transport and DNA replication and repair in larvae compared to the Cu group. This may have further interfered with the normal physiological activities of S. esculenta larvae. Overall, at high temperatures, Cu exposure induces a more intense inflammatory response. The results of this study provide a theoretical foundation for researchers to further understand the effects of environmental factors on the immunity of S. esculenta larvae, as well as preliminary insights into the enhanced toxic effects of metallic copper on aquatic organisms under high-temperature conditions.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"262"},"PeriodicalIF":3.5,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143647214","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":"TransGeneSelector: using a transformer approach to mine key genes from small transcriptomic datasets in plant responses to various environments.","authors":"Kerui Huang, Jianhong Tian, Lei Sun, Haoliang Hu, Xuebin Huang, Shiqi Zhou, Aihua Deng, Zhibo Zhou, Ming Jiang, Guiwu Li, Peng Xie, Yun Wang, Xiaocheng Jiang","doi":"10.1186/s12864-025-11434-y","DOIUrl":"https://doi.org/10.1186/s12864-025-11434-y","url":null,"abstract":"<p><p>Gene mining is crucial for understanding the regulatory mechanisms underlying complex biological processes, particularly in plants responding to environmental conditions. Traditional machine learning methods, while useful, often overlook important gene relationships due to their reliance on manual feature selection and limited ability to capture complex inter-gene regulatory dynamics. Deep learning approaches, while powerful, are often unsuitable for small sample sizes. This study introduces TransGeneSelector, the first deep learning framework specifically designed for mining key genes from small transcriptomic datasets. By integrating a Wasserstein Generative Adversarial Network with Gradient Penalty (WGAN-GP) for sample generation and a Transformer-based network for classification, TransGeneSelector efficiently addresses the challenges of small-sample transcriptomic data, capturing both global gene regulatory interactions and specific biological processes. Evaluated in Arabidopsis thaliana, the model achieved high classification accuracy in predicting seed germination and heat stress conditions, outperforming traditional methods like Random Forest and Support Vector Machines (SVM). Moreover, Shapley Additive Explanations (SHAP) analysis and gene regulatory network construction revealed that TransGeneSelector effectively identified genes that appear to have upstream regulatory functions based on our analyses, enriching them in multiple key pathways which are critical for seed germination and heat stress response. RT-qPCR validation further confirmed the model's gene selection accuracy, demonstrating consistent expression patterns across varying germination conditions. The findings underscore the potential of TransGeneSelector as a robust tool for gene mining, offering deeper insights into gene regulation and organism adaptation under diverse environmental conditions. This work provides a framework that leverages deep learning for key gene identification in small transcriptomic datasets.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"259"},"PeriodicalIF":3.5,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143647189","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 TaFDL gene family responded to vernalization in wheat (Triticum aestivum L.).","authors":"Wenjie Kan, Yameng Gao, Yan Zhu, Ziqi Wang, Zhu Yang, Yuan Cheng, Jianjun Guo, Dacheng Wang, Caiguo Tang, Lifang Wu","doi":"10.1186/s12864-025-11436-w","DOIUrl":"https://doi.org/10.1186/s12864-025-11436-w","url":null,"abstract":"<p><strong>Background: </strong>FLOWERING LOCUS D (FD) is a basic leucine zipper (bZIP) transcription factor known to be crucial in vernalization, flowering, and stress response across a variety of plants, including biennial and winter annual species. The TaFD-like (TaFDL) gene in wheat is the functional homologue of Arabidopsis FD, yet research on the TaFDL gene family in wheat is still lacking.</p><p><strong>Results: </strong>In this study, a total of 62 TaFDL gene family members were identified and classified into 4 main subfamilies, and these genes were located on 21 chromosomes. A comprehensive analysis of the basic physicochemical properties, gene structure, conservation motif, conserved domain, and advanced protein structure of TaFDL gene family revealed the conservation among its individual subfamily. The family members underwent purifying selection. The segmental duplication events were the main driving force behind the expansion of the TaFDL gene family. The TaFDL gene family underwent differentiation in the evolution of FD genes. Additionally, the subcellular localization and transcriptional activation activities of five key TaFDL members were demonstrated. Gene Ontology (GO) annotations and promoter cis-regulatory element analysis indicated that the TaFDL members may play potential roles in regulating flowering, hormone response, low-temperature response, light response, and stress response, which were verified by transcriptome data analysis. Specifically, quantitative real-time PCR (qRT-PCR) analysis revealed that five TaFDL genes exhibited differential responses to different vernalization conditions in winter wheat seeding. Finally, the homologous genes of the five key TaFDL genes across nine different wheat cultivars highlight significant genetic diversity.</p><p><strong>Conclusion: </strong>These findings enrich the research on FD and its homologous genes, providing valuable insights into the TaFDL gene family's response to vernalization.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"255"},"PeriodicalIF":3.5,"publicationDate":"2025-03-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143647170","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":"Single specimen genome assembly of Culicoides stellifer shows evidence of a non-retroviral endogenous viral element.","authors":"Jessica Castellanos-Labarcena, Yoamel Milián-García, Tyler A Elliott, Dirk Steinke, Robert Hanner, Sarah J Adamowicz","doi":"10.1186/s12864-025-11449-5","DOIUrl":"10.1186/s12864-025-11449-5","url":null,"abstract":"<p><strong>Background: </strong>Advancing our knowledge of vector species genomes is a key step in our battle against the spread of diseases. Biting midges of the genus Culicoides are vectors of arboviruses that significantly affect livestock worldwide. Culicoides stellifer is a suspected vector with a wide range distribution in North America, for which cryptic diversity has been described.</p><p><strong>Results: </strong>With just one specimen of C. stellifer, we assembled and annotated the nuclear and mitochondrial genome using the ultra-low input DNA PacBio protocol. The genome assembly is 119 Mb in length with a contig N50 value of 479.3 kb, contains 11% repeat sequences and 18,895 annotated protein-coding genes. To further elucidate the role of this species as a vector, we provide genomic evidence of a non-retroviral endogenous viral element integrated into the genome that corresponds to rhabdovirus nucleocapsid proteins, the same family as the vesicular stomatitis virus.</p><p><strong>Conclusions: </strong>This genomic information will pave the way for future investigations into this species's putative vector role. We also demonstrate the practicability of completing genomic studies in small dipterans using single specimens preserved in ethanol as well as introduce a workflow for data analysis that considers the challenges of insect genome assembly.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"247"},"PeriodicalIF":3.5,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11907880/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143633408","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":"Whole transcriptome analysis in oviduct provides insight into microRNAs and ceRNA regulative networks that targeted reproduction of goat (Capra hircus).","authors":"Qingqing Liu, Zhipeng Sun, Yufang Liu, Xiaoyun He, Chunhuan Ren, Xiangyu Wang, Ran Di, Yongju Zhao, Zijun Zhang, Mingxing Chu","doi":"10.1186/s12864-025-11438-8","DOIUrl":"10.1186/s12864-025-11438-8","url":null,"abstract":"<p><strong>Background: </strong>Reproduction traits are crucial for livestock breeding and represent key economic indicators in the domestic goat (Capra hircus) industry. The oviduct, a critical organ in female mammals, plays a pivotal role in several reproductive processes; however, its molecular mechanisms remain largely unknown. Non-coding RNA and mRNAs are essential regulatory elements in reproductive processes; yet their specific roles and regulatory networks in goat oviducts remain unclear.</p><p><strong>Results: </strong>In this study, we conducted small RNA sequencing of the oviduct in high- and low-fecundity goats during the follicular (FH and FL groups, n = 10) and luteal (LH and LL groups, n = 10) phase, profiling 20 tissue samples. Combinatorial whole-transcriptome expression profiles were applied to the same samples to uncover the competitive endogenous RNA (ceRNA) regulation network associated with goat fecundity. RT-qPCR was employed to validate the miRNA profiling results, and ceRNA regulatory networks were analyzed through luciferase assay. Gene set enrichment analysis (GSEA) confirmed that the cytokine-cytokine receptor interaction and TGF-β signaling pathway, both related to embryonic development, were enriched in DEM target genes. Additionally, miR-328-3p, a core miRNA, targets SMAD3 and BOP1, which are involved in the negative regulation of cell growth and embryonic development. TOB1 and TOB2, targeted by miR-204-3p, regulate cell proliferation via the protein kinase C-activating G-protein coupled receptor signaling pathway. Analyses of ceRNA regulatory networks revealed that LNC_005981 - miR-328-3p - SMAD3 and circ_0021923 - miR-204-3p - DOT1L may affect goats' reproduction, findings that were validated using luciferase assay.</p><p><strong>Conclusion: </strong>Analysis of whole-transcriptome profiling of goat oviducts identified several key miRNAs and ceRNAs that may regulate oocyte maturation, embryo development, and the interactions between the oviduct and gametes/early embryos, providing insights into the molecular mechanisms of reproductive regulatory networks.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"250"},"PeriodicalIF":3.5,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11907954/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143633467","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 genomics reveals the high diversity and adaptation strategies of Polaromonas from polar environments.","authors":"Yuntong Du, Changhua He, Karen G Lloyd, Tatiana A Vishnivetskaya, Hongpeng Cui, Bing Li, Da Gong, Xiaopeng Fan, Dayi Zhang, Hongchen Jiang, Renxing Liang","doi":"10.1186/s12864-025-11410-6","DOIUrl":"10.1186/s12864-025-11410-6","url":null,"abstract":"<p><strong>Background: </strong>Bacteria from the genus Polaromonas are dominant phylotypes found in a variety of low-temperature environments in polar regions. The diversity and biogeographic distribution of Polaromonas have been largely expanded on the basis of 16 S rRNA gene amplicon sequencing. However, the evolution and cold adaptation mechanisms of Polaromonas from polar regions are poorly understood at the genomic level.</p><p><strong>Results: </strong>A total of 202 genomes of the genus Polaromonas were analyzed, and 121 different species were delineated on the basis of average nucleotide identity (ANI) and phylogenomic placements. Remarkably, 8 genomes recovered from polar environments clustered into a separate clade ('polar group' hereafter). The genome size, coding density and coding sequences (CDSs) of the polar group were significantly different from those of other nonpolar Polaromonas. Furthermore, the enrichment of genes involved in carbohydrate and peptide metabolism was evident in the polar group. In addition, genes encoding proteins related to betaine synthesis and transport were increased in the genomes from the polar group. Phylogenomic analysis revealed that two different evolutionary scenarios may explain the adaptation of Polaromonas to cold environments in polar regions.</p><p><strong>Conclusions: </strong>The global distribution of the genus Polaromonas highlights its strong adaptability in both polar and nonpolar environments. Species delineation significantly expands our understanding of the diversity of the Polaromonas genus on a global scale. In this study, a polar-specific clade was found, which may represent a specific ecotype well adapted to polar environments. Collectively, genomic insight into the metabolic diversity, evolution and adaptation of the genus Polaromonas at the genome level provides a genetic basis for understanding the potential response mechanisms of Polaromonas to global warming in polar regions.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"248"},"PeriodicalIF":3.5,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11907789/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143633423","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}