BMC Biology最新文献

{"title":"Comparative macrogenomics reveal plateau adaptation of gut microbiome in cervids.","authors":"Bin Li, Yuangang Yang, Bo Xu, Pengfei Song, Feng Jiang, Hongmei Gao, Zhenyuan Cai, Haifeng Gu, Tongzuo Zhang","doi":"10.1186/s12915-025-02269-w","DOIUrl":"10.1186/s12915-025-02269-w","url":null,"abstract":"<p><strong>Background: </strong>Diverse gut microbiota in animals significantly influences host physiology, ecological adaptation, and evolution. However, the specific functional roles of gut microbiota in facilitating host adaptation, as well as the coevolutionary dynamics between microbiota and their hosts, remain largely understudied.</p><p><strong>Results: </strong>A total of 41,847 metagenome-assembled genomes and 3193 high-quality species-level genome bins were generated, establishing a comprehensive gut microbiome catalog for cervids in this study. Phylogenetic analysis revealed a coevolutionary relationship between cervids and their gut microbiota. Comparative metagenomic analyses further indicated that the gut microbiota of plateau cervids have undergone genome-level adaptations related to energy metabolism. At the genus level, species-level genome bins from the genera Alistipes and Faecousia in plateau cervids exhibit enhanced energy metabolism capabilities. Structural variations analysis revealed that the insertion and duplications structural variations in the gut microbiota of plateau cervids were significantly enriched in energy metabolism pathways. In contrast, the deletions and contractions in structural variations were predominantly enriched with metabolic pathways involved in the biosynthesis of diverse biochemical molecules.</p><p><strong>Conclusions: </strong>Our study provides a comprehensive gut microbiome catalog of the cervid gut microbiota, revealing the coevolutionary relationship between cervid gut microbiota and hosts. These findings highlight the adaptive genomic evolution of the gut microbiota in contributing to the plateau adaptability of cervids and offer new insights into the mechanisms by which the gut microbiota help hosts adapt to extreme environments.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"23 1","pages":"154"},"PeriodicalIF":4.4,"publicationDate":"2025-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12139185/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144224390","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The origin and evolution of cultivated rice and genomic signatures of heterosis for yield traits in super-hybrid rice.","authors":"Yiyong Zhao, Tao Li, Daliang Liu, Hao Yin, Liang Wang, Song Lu, Houlin Yu, Xinhao Sun, Taikui Zhang, Quanzhi Zhao","doi":"10.1186/s12915-025-02255-2","DOIUrl":"10.1186/s12915-025-02255-2","url":null,"abstract":"<p><strong>Background: </strong>Understanding the evolutionary history of cultivated rice (Oryza sativa) and the genomic basis of heterosis is crucial for advancing rice productivity and ensuring global food security. The origins of the two main subspecies, indica and japonica, remain contentious, with debates over single versus multiple domestication events. Additionally, the genetic mechanisms underlying heterosis in elite super-hybrid rice varieties are not fully elucidated.</p><p><strong>Results: </strong>We performed a comprehensive genome-scale phylogenomic analysis using 33 high-quality Oryzeae genomes, integrating 39,984 gene trees. Our findings support the independent origins of indica and japonica subspecies, with molecular dating and synonymous substitution rates indicating nearly synchronous evolutionary trajectories. Analysis of 1383 gene duplications in the common ancestor of O. sativa revealed their involvement in vital biological processes and environmental adaptability. Phylogenomic analyses revealed no significant genomic signatures indicative of extensive hybridization events between the progenitors of indica and japonica. Newly generated 71.67 Gb of whole-genome sequencing data of five elite super-hybrid rice varieties and their progenitors uncovered differential positive selection and genetic exchanges between subspecies, contributing to heterosis formation. Transcriptome analyses highlighted the predominance of non-additive gene expression in heterosis, especially in genes related to DNA repair and recombination. Furthermore, expression quantitative trait locus (eQTL) and de novo mutation analyses identified key developmental and stress response genes, offering potential targets for enhancing heterosis.</p><p><strong>Conclusions: </strong>Our study provides robust evidence for the independent domestication of indica and japonica rice subspecies and elucidates the genomic features associated with heterosis in super-hybrid rice. By identifying key genes linked to adaptability and heterosis, we offer valuable insights and genetic resources for breeding programs aimed at improving rice yield and resilience. These findings enhance our understanding of rice evolution and the complex genetic factors driving heterosis, contributing to future strategies for agricultural productivity enhancement.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"23 1","pages":"153"},"PeriodicalIF":4.4,"publicationDate":"2025-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12139199/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144224350","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"High resolution of full-length RNA sequencing deciphers massive transcriptome complexity during zebrafish embryogenesis.","authors":"Jing Bo, Wenyu Fang, Jing Wang, Shunping He, Liandong Yang","doi":"10.1186/s12915-025-02271-2","DOIUrl":"10.1186/s12915-025-02271-2","url":null,"abstract":"<p><strong>Background: </strong>The zebrafish has significantly advanced our understanding of human disease and development, with nearly 70% of single-copy protein-coding genes conserved between the species. However, research on zebrafish is limited by gaps in existing genome annotations, which are primarily based on computational predictions and short-read sequencing data.</p><p><strong>Results: </strong>To address this issue, we employed the PacBio Sequel II platform to generate a time-series full-length transcriptome landscape of zebrafish embryogenesis, covering 21 time points from embryo to six days post-fertilization. Our analysis uncovered 2113 previously unannotated genes and 33,018 novel isoforms of previously annotated genes, substantially expanding the current zebrafish gene annotations. We verified these findings using various methods, including domain prediction, homology analysis, conservation analysis, transcript quantification with short-read RNA-seq, and promoter position information with H3K4me3 and CAGE-seq. Furthermore, we analyzed the dynamic expression of transcripts across the 21 developmental stages using next-generation sequencing data, identifying variable splicing events throughout these stages.</p><p><strong>Conclusions: </strong>Collectively, our study provides a high-resolution and significantly improved transcriptome annotation during zebrafish embryogenesis, offering a valuable resource for the zebrafish research community.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"23 1","pages":"155"},"PeriodicalIF":4.4,"publicationDate":"2025-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12139336/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144224349","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evaluating conservation gaps of China's national key protected wild plants: insights from county-level distribution data.","authors":"Xiaotian Pan, Zhangjian Shan, Xin Tian, Yanting Niu, Yun Liu, Zhe Li, Yutong Li, Yuxi Huang, Jianfei Ye","doi":"10.1186/s12915-025-02270-3","DOIUrl":"10.1186/s12915-025-02270-3","url":null,"abstract":"<p><strong>Background: </strong>The National Key Protected Wild Plants (NKPWPs) list serves as China's primary legal framework for plant diversity protection, with the species categorized into Level I (critically endangered, strictly protected) and Level II (lower risk but still requiring protection). However, the geographical distribution of these species and gaps in their conservation remain elusive due to the limited availability of data on species distribution. Thus, to address these gaps and support precise conservation, we developed a county-level distribution database for the NKPWP species using information primarily sourced from literature. Using this database, we elucidated the geographical distribution patterns of NKPWPs and identified the gaps in both in situ and ex situ conservation.</p><p><strong>Results: </strong>The NKPWPs analyzed in the study included 1,128 plant species. We compiled a county-level distribution database for these species with 30,397 records. Detailed analysis of this data revealed that these species were concentrated in the mountainous regions of southern China, including the Eastern Himalaya-Hengduan Mountains, south Yunnan, the Yunnan-Guizhou-Guangxi border, and the Wuling Mountains. Among the 1,118 embryophyte species of the checklist, 1,060 (94.81%) were found conserved in situ, 681 (60.91%) were found conserved ex situ, and 660 (59.03%) through both approaches. Besides, species with a higher threat level and limited distribution range exhibited lower conservation coverage in both ex situ and in situ approaches; 37 species received no conservation (3.31%).</p><p><strong>Conclusions: </strong>The county-level distribution database developed in this study comprehensively depicts the geographical distribution patterns of NKPWP in China, offering valuable data for planning species conservation and providing a foundational framework for addressing the existing gaps in their conservation across China. This database will ultimately support targeted conservation and resource allocation to protect plant diversity effectively. We also suggest adopting an integrated evaluation approach for conservation strategies in other areas, globally, or for other biological groups.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"23 1","pages":"156"},"PeriodicalIF":4.4,"publicationDate":"2025-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12139105/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144224391","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular basis governing diapause and pigmentation in the hawthorn spider mite, Amphitetranychus viennensis.","authors":"Jing Yang, Yuanpeng Duan, Yifei Wang, Yuying Zhang, Meibin Liu, Zhonghuan Zhang, Xuguo Zhou, Meifeng Ren","doi":"10.1186/s12915-025-02258-z","DOIUrl":"10.1186/s12915-025-02258-z","url":null,"abstract":"<p><strong>Background: </strong>Diapause is a physiological adaptation that evolves in arthropods to cope with unfavorable environmental conditions. By synchronizing their development and reproduction to seasonal variations, these animals can maximize their odds to survive adverse conditions. Among the environmental cues that trigger diapause, photoperiod is the most extensively studied. The hawthorn spider mite, Amphitetranychus viennensis, is one of the most devastating arthropod pests in fruit trees and woody ornamental plants. Overwintering females undergo a reproductive facultative diapause when A. viennensis immatures are exposed to long nights, which is consistent with the two-spotted spider mite, Tetranychus urticae. However, the molecular mechanisms underlying diapause in A. viennensis remain unexplored.</p><p><strong>Results: </strong>Here, we first developed a photoperiodic diapause bioassay for A. viennensis and identified protochrysalis, a non-feeding resting stage between the larva and protonymph, as a crucial developmental stage for diapause induction. We then identified six genes related to the carotenoid pathway, including three involved in synthesis, AvPD, AvLC/PS1, and AvLC/PS2, and the other three associated with metabolism, AvBCO1, AvBCO2, and AvCYP384A1. Phylogenetic analysis suggested that AvPD, AvLC/PS1, and AvLC/PS2 were acquired through horizontal transfer from fungi. Finally, functional characterization using RNA interference (RNAi) demonstrated that AvPD, AvLC/PS1, AvBCO2, and AvCYP384A1 contribute to pigmentation, while AvPD, AvLC/PS1, and AvBCO1 are involved in the regulation of diapause in A. viennensis.</p><p><strong>Conclusions: </strong>This study not only advances our current knowledge on the molecular basis governing pigmentation and diapause, but also sheds light on the development of long-term sustainable management strategies for these polyphagous herbivores in spider mites in general and A. viennensis in particular.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"23 1","pages":"152"},"PeriodicalIF":4.4,"publicationDate":"2025-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12135272/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144214998","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Co-opted and canonical glycerol channels play a major role during anhydrobiosis of an extremophile crustacean.","authors":"Ángel Rey-Alfonso, José Luis Maestro, François Chauvigné, Jèssica Gómez-Garrido, Tyler Alioto, Peter Bossier, Roderick Nigel Finn, Joan Cerdà","doi":"10.1186/s12915-025-02262-3","DOIUrl":"10.1186/s12915-025-02262-3","url":null,"abstract":"<p><strong>Background: </strong>Extremophiles evolved capacities to survive extended exposure to harsh environmental conditions such as complete desiccation (anhydrobiosis) and freezing (cryobiosis). Accumulation of the three-carbon polyhydric alcohol glycerol is commonly observed in anhydrobiotic organisms, although it is considered to preferentially enhance cryobiosis rather than anhydrobiosis.</p><p><strong>Results: </strong>Here, using dormant stages of the halophilic extremophile crustacean Artemia franciscana, we show that this role is reversed. We find that A. franciscana and related branchiopods evolved co-opted entomoglyceroporin (Eglp)-like aquaporin-type channels previously only characterized in hexapods. Phylogenomic and site-directed mutagenesis analyses indicate that EglpL orthologs likely evolved during the early Cambrian in the common ancestor of the Pancrustacea. RNAi-mediated knockdown experiments show that the A. franciscana EglpL glycerol transporter is subfunctionally co-regulated with canonical aquaglyceroporins (Glps) to mediate glycerol accumulation in the diapause cysts. Termination of diapause using either desiccation or hydrogen peroxide and further exposure of the cysts to freezing suggest that the acquired glycerol plays a more critical role in anhydrobiosis rather than cryobiosis.</p><p><strong>Conclusions: </strong>These findings uncover the essential role of evolutionary divergent aquaporin-type glycerol channels in the accrual of glycerol in an anhydrobiotic organism and reveal a previously overlooked function of this polyol for desiccation tolerance.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"23 1","pages":"151"},"PeriodicalIF":4.4,"publicationDate":"2025-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12135271/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144214997","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Circannual breeding and methylation are impacted by the equinox in Peromyscus.","authors":"Kim-Tuyen Huynh-Dam, Celia Jaeger, Asieh Naderi, M Furkan Bayram, Janet P Crossland, Vimala Kaza, Shayne Barlow, Ioulia Chatzistamou, Anthony Long, Steve Horvath, Hippokratis Kiaris","doi":"10.1186/s12915-025-02251-6","DOIUrl":"10.1186/s12915-025-02251-6","url":null,"abstract":"<p><strong>Background: </strong>Photoperiod is the major regulator of circannual patterns in mammals, but at animal facilities, despite the controlled conditions, some rodents still exhibit seasonality in their breeding. By evaluating more than 97,000 breeding records of closed Peromyscus colonies, we explored if seasonal breeding patterns exist in animals maintained for several decades at controlled environments.</p><p><strong>Results: </strong>Seasonal preferences for offspring production were recorded that depended on maternal birth month. Birth in March and September, especially of mothers, showed best fit in 12-knots generalized additive models, implying that the memory of birth month is more intensively carried during the Spring and Autumn equinoxes. The memory of birth month was associated with circannual CpG methylation at birth and revealed that most intense differential methylation, primarily demethylation, occurs in animals that were born in September. Comparison of breeding performance in the periods between the equinoxes showed preference for summer littering by the winter-born animals, especially in the polygamous P. maniculatus bairdii and P. leucopus stocks, and at least in the former species, this was associated with longer estrus cycles. Genes associated with differentially methylated CpGs in winter and summer periods in polygamous species pointed to regulation of gonadotropin hormone releasing hormone secretion. Birth at individually ventilated cages disrupted methylation profiles.</p><p><strong>Conclusions: </strong>The cyclicity of breeding and methylation patterns suggest that signals other than the photoperiod regulate circannual patterns in deer mice, that reset in the equinox especially in autumn, and that the females are more sensitive to these signals than males.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"23 1","pages":"149"},"PeriodicalIF":4.4,"publicationDate":"2025-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12131350/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144207797","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Latitude-driven adaptive evolution of body length in diverse pig breeds across China.","authors":"Yifei Wang, Ran Feng, Xiao Hu, Dai Shan, Xukun Zhang, Yuwei Gou, Ting Zheng, Yujing Li, Kaixin Fei, Qibin Zhang, Zhengyin Gong, Yanzhi Jiang","doi":"10.1186/s12915-025-02265-0","DOIUrl":"10.1186/s12915-025-02265-0","url":null,"abstract":"<p><strong>Background: </strong>The geographical divergence of Chinese pigs led to various phenotypes through adaptive evolution. In particular, pigs from relatively low altitudes exhibit a positive correlation between body length and latitude. However, the molecular mechanisms underlying this relationship remain unclear. Identifying candidate genes associated with this body length variation is crucial for further understanding the genetic basis of adaptive traits in these Chinese pig breeds.</p><p><strong>Results: </strong>We assembled a high-quality genome of the Neijiang pig as benchmark and analyse 297 Chinese domestic pigs and six Chinese wild boars distributed across different latitudes. Our study provides a comprehensive assessment of genetic diversity and population structure, revealing distinct genetic backgrounds of Chinese indigenous pigs from different regions. Most importantly, we observed a strong correlation between latitude and body length, and screened out the AFF4 gene through four calculation methods. Meanwhile, gene introgression and haplotype divergence of AFF4 among low-altitude pig breeds also proved that AFF4 may be one of the driver genes affecting the adaptive evolution of pig body length. Overexpression and knockdown experiments were performed in our study and confirmed the significantly impact of AFF4 on the osteogenic differentiation process.</p><p><strong>Conclusions: </strong>These results enrich the pig genome pool, offer a comprehensive understanding of genetic architecture for Chinese pig breeds, and shed light on the correlation between latitude and body length of adaptive evolution of Chinese pigs.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"23 1","pages":"150"},"PeriodicalIF":4.4,"publicationDate":"2025-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12131766/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144207798","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A multi-tissue atlas of allelic-specific expression reveals the characteristics, mechanisms, and relationship with dominant effects in cattle.","authors":"Jiaqi Li, Lei Xu, Xiaoyun Liang, Letian Li, Frederic Farnir, Xixia Huang, Qiuming Chen","doi":"10.1186/s12915-025-02257-0","DOIUrl":"10.1186/s12915-025-02257-0","url":null,"abstract":"<p><strong>Background: </strong>Allele-specific expression (ASE) analysis is a crucial tool for validating expression quantitative trait loci (eQTLs), identifying causal variants associated with complex traits, and investigating the genetic mechanisms underlying heterosis. In this study, we characterized ASE variants across 35 tissues using 7532 publicly available RNA-seq datasets. Additionally, we explored the mechanisms driving ASE through integration with epigenomic data and examined the relationship between ASE and dominance effects on gene expression and milk-related traits in Holstein cattle.</p><p><strong>Results: </strong>ASE variants exhibited stronger tissue specificity and lower reproducibility compared to eQTLs. Interestingly, variants with opposite directional effects demonstrated greater resilience across diverse environments. Functional annotation revealed that ASE variants were enriched in both enhancer and promoter regions during transcription and implicated in post-transcriptional and translational processes, including mutations that affect mRNA splicing and trigger nonsense-mediated decay. Analysis of eQTLs, splicing QTLs (sQTLs), and validated QTLs associated with milk-related traits in Holstein cattle, coupled with enrichment analysis in QTL databases and effect size evaluation, indicated that ASE variants were more closely aligned with dominant effects than additive effects, particularly in reproductive and immune-related tissues/traits, which exhibited higher levels of heterosis.</p><p><strong>Conclusions: </strong>Our findings not only enhance our understanding of the genetic mechanisms underlying heterosis and ASE formation but also provide a valuable resource of regulatory variants that can be leveraged to improve economic traits through molecular breeding or the strategic exploitation of heterosis.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"23 1","pages":"148"},"PeriodicalIF":4.4,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12123890/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144181271","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"annATAC: automatic cell type annotation for scATAC-seq data based on language model.","authors":"Lingyu Cui, Fang Wang, Hongfei Li, Qiaoming Liu, Murong Zhou, Guohua Wang","doi":"10.1186/s12915-025-02244-5","DOIUrl":"10.1186/s12915-025-02244-5","url":null,"abstract":"<p><strong>Background: </strong>Cell type annotation serves as the cornerstone for downstream analysis of single cell data. Nevertheless, scATAC-seq data is characterized by high sparsity and dimensionality, presenting significant challenges to its annotation process.</p><p><strong>Results: </strong>We introduce a novel method based on language model, named annATAC, which is designed for the automatic annotation of cell types in scATAC-seq data. This method primarily consists of three stages. During the pre-training stage, by training on a vast amount of unlabeled data, the model can learn the interaction relationships between peaks, thus building a preliminary understanding of the data features. Subsequently, in the fine-tuning stage, a small quantity of labeled data is utilized to conduct secondary training on the model, which enables the model to identify cell types accurately. Finally, in the prediction stage, the trained model is applied to annotate scATAC-seq data.</p><p><strong>Conclusions: </strong>Compared with other automatic annotation methods across multiple datasets, annATAC demonstrates superiority on the annotation performance. Further experiments have validated that annATAC holds great potential in identifying marker peaks and marker motifs. It is expected that annATAC will provide more profound and precise analysis outcomes for scATAC-seq research. As a result, it will effectively promote the progress of relevant biomedical research.</p>","PeriodicalId":9339,"journal":{"name":"BMC Biology","volume":"23 1","pages":"145"},"PeriodicalIF":4.4,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12121080/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144172787","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}