Genome Biology最新文献

{"title":"The 5-methylcytosine DNA glycosylase ROS1 prevents paternal genome hypermethylation in Arabidopsis endosperm","authors":"Elizabeth A. Hemenway, Mary Gehring","doi":"10.1186/s13059-025-03745-w","DOIUrl":"https://doi.org/10.1186/s13059-025-03745-w","url":null,"abstract":"DNA methylation patterning is a consequence of opposing activities of DNA methyltransferases and DNA demethylases. In many plant and animal species, reproduction is a period of significant epigenome lability. In flowering plants, two distinct female gametes, the egg cell and the central cell, are fertilized to produce the embryo and the endosperm of the seed. The endosperm is an unusual tissue, exemplified by triploidy and reduced DNA methylation. In Arabidopsis thaliana, a 5-methylcytosine DNA glycosylase, DME, demethylates regions of the central cell genome, leading to methylation differences between maternally- and paternally-inherited endosperm genomes after fertilization. Expression of DME in the central cell is required for gene imprinting, or parent-of-origin specific gene expression, in endosperm. DME is part of a four member gene family in Arabidopsis that includes ROS1, DML2, and DML3. It is unknown whether any of the other DNA glycosylases are required for endosperm methylation patterning. Using whole-genome methylation profiling, we identify ROS1 target regions in the endosperm. We show that ROS1 prevents hypermethylation of paternally-inherited alleles in the endosperm at regions that lack maternal or paternal allele methylation in wild-type endosperm. Additionally, we demonstrate that at many ROS1 target regions the maternal alleles are demethylated by DME. ROS1 promotes epigenetic symmetry between parental genomes in the endosperm by preventing CG methylation gain on the paternal genome. We conclude that ROS1 and DME act in a parent-of-origin-specific manner at shared endosperm targets, and consider possible implications for the evolution of imprinting mechanisms.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"82 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145077420","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A compendium of synthetic lethal gene pairs defined by extensive combinatorial pan-cancer CRISPR screening","authors":"Victoria Harle, Victoria Offord, Birkan Gökbağ, Lazaros Fotopoulos, Thomas Williams, Diana Alexander, Ishan Mehta, Nicola A. Thompson, Rebeca Olvera-León, Stefan Peidli, Vivek Iyer, Emanuel Gonçalves, Narod Kebabci, Barbara De Kegel, Joris van de Haar, Lang Li, Colm J. Ryan, David J. Adams","doi":"10.1186/s13059-025-03737-w","DOIUrl":"https://doi.org/10.1186/s13059-025-03737-w","url":null,"abstract":"Synthetic lethal interactions are attractive therapeutic candidates as they enable selective targeting of cancer cells in which somatic alterations have disrupted one member of a synthetic lethal gene pair while leaving normal tissues untouched, thus minimising off-target toxicity. Despite this potential, the number of well-established and validated synthetic lethal gene pairs is modest. We generate a dual-guide CRISPR/Cas9 Library and analyse 472 predicted synthetic lethal pairs in 27 cancer cell Lines from melanoma, pancreatic and lung cancer Lineages. We report a robust collection of 117 genetic interactions within and across cancer types and explore their candidacy as therapeutic targets. We show that SLC25A28 is an attractive target since its synthetic lethal paralog partner SLC25A37 is homozygously deleted pan-cancer. We generate knockout mice for Slc25a28 revealing that, except for cataracts in some mice, these animals are normal; suggesting inhibition of SLC25A28 is unlikely to be associated with profound toxicity. We provide and validate an extensive collection of synthetic lethal interactions across cancer types.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"76 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145077751","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A comprehensive benchmarking of adaptive sampling tools for nanopore sequencing","authors":"Lang Yang, Yanfeng Lin, Peihan Li, Kaiying Wang, Jinhui Li, Yuqi Liu, Xiaochen Bo, Ming Ni, Peng Li, Hongbin Song","doi":"10.1186/s13059-025-03729-w","DOIUrl":"https://doi.org/10.1186/s13059-025-03729-w","url":null,"abstract":"Adaptive sampling is an emerging technology to enrich target reads while depleting unwanted reads during real-time nanopore sequencing. The application of different algorithms has spawned various tools for the determination of read rejection. However, an evaluation in conjunction with identifying the optimal enrichment performance for a specific task has yet to be conducted. This study aimed to evaluate the performance of six widely used tools for nanopore adaptive sampling. Three distinct types of tasks were selected for testing, including the intraspecies enrichment of COSMIC genes, the interspecies enrichment of Saccharomyces cerevisiae, and the depletion of human host DNA. All the tools show increases in coverage depths of targets varying from 1.50- to 4.86-fold. The combination of Guppy for base calling and minimap2 for read alignment emerged as the optimal read classification strategy with the highest accuracy. MinKNOW, Readfish, and BOSS-RUNS using this strategy show generally excellent enrichment or depletion performance. The deep learning method utilizing raw signals demonstrates higher accuracy and quicker read ejection compared to the conventional signal-based approach, also achieving top-class performance in host depletion. Our benchmarking study conducted a thorough comparison of current tools on various adaptive sampling occasions. The nucleotide-alignment-based approach is capable of handling diverse target references with broad application. The tools employing this strategy, especially MinKNOW, could be considered as a prior option for most adaptive sampling scenarios. The deep learning technique utilizing raw signals demonstrates remarkable classification efficiency and accuracy, warranting greater emphasis and exploration in future software development endeavors.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"36 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145071925","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Predicting the structural impact of human alternative splicing","authors":"Yuxuan Song, Chengxin Zhang, Gilbert S. Omenn, Matthew J. O’Meara, Joshua D. Welch","doi":"10.1186/s13059-025-03744-x","DOIUrl":"https://doi.org/10.1186/s13059-025-03744-x","url":null,"abstract":"Protein structure prediction with neural networks is a powerful new method for linking protein sequence, structure, and function, but structures have generally been predicted for only a single isoform of each gene, neglecting splice variants. To investigate the structural implications of alternative splicing, we use AlphaFold2 to predict the structures of more than 11,000 human isoforms. We employ multiple metrics to identify splicing-induced structural alterations, including template matching score, secondary structure composition, surface charge distribution, radius of gyration, accessibility of post-translational modification sites, and structure-based function prediction. We identify examples of how alternative splicing induces clear changes in each of these properties. Structural similarity between isoforms largely correlates with degree of sequence identity, but we identify a subset of isoforms with low structural similarity despite high sequence similarity. Exon skipping and alternative last exons tend to increase the surface charge and radius of gyration. Splicing also buries or exposes numerous post-translational modification sites, most notably among the isoforms of BAX. Functional prediction identifies numerous functional differences between isoforms of the same gene, with loss of function compared to the reference predominating. Finally, we use single-cell RNA-seq data from the Tabula Sapiens to determine the cell types in which each structure is expressed. Our work represents an important resource for studying the structure and function of splice isoforms across the cell types of the human body.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"17 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145071923","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A hierarchical, count-based model highlights challenges in scATAC-seq data analysis and points to opportunities to extract finer-resolution information","authors":"Aaron Wing Cheung Kwok, Heejung Shim, Davis J. McCarthy","doi":"10.1186/s13059-025-03735-y","DOIUrl":"https://doi.org/10.1186/s13059-025-03735-y","url":null,"abstract":"Data from Single-cell Assay for Transposase Accessible Chromatin with Sequencing (scATAC-seq) is highly sparse. While current computational methods feature a range of transformation procedures to extract meaningful information, major challenges remain. Here, we discuss the major scATAC-seq data analysis challenges such as sequencing depth normalization and region-specific biases. We present a hierarchical count model that is motivated by the data generating process of scATAC-seq data. Our simulations show that current scATAC-seq data, while clearly containing physical single-cell resolution, are too sparse to infer true informational-level single-cell, single-region of chromatin accessibility states. While the broad utility of scATAC-seq at a cell type level is undeniable, describing it as fully resolving chromatin accessibility at single-cell resolution, particularly at individual locus level, may overstate the level of detail currently achievable. We conclude that chromatin accessibility profiling at true single-cell, single-region resolution is challenging with current data sensitivity, but that it may be achieved with promising developments in optimizing the efficiency of scATAC-seq assays.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"16 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145071924","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Author Correction: cuteFC: regenotyping structural variants through an accurate and efficient force-calling method","authors":"Tao Jiang, Shuqi Cao, Yadong Liu, Zhendong Zhang, Bo Liu, Ruibang Luo, Guohua Wang, Yadong Wang","doi":"10.1186/s13059-025-03726-z","DOIUrl":"https://doi.org/10.1186/s13059-025-03726-z","url":null,"abstract":"<p><b>Author Correction: Genome Biol 26, 166 (2025)</b></p><p><b>https://doi.org/10.1186/s13059-025-03642-2</b></p><br/><p>Following publication of the original article [1], the authors identified three errors in <i>Methods</i> and <i>Funding, and Fig. 2D</i>.</p><p>1. In the original version, the total number of simulated structural variations was incorrectly stated as 3,668 in the <i>Process the benchmarking datasets</i> part of <i>Methods</i> section. The correct sum of the simulated SVs: 2,191 insertions, 1,333 deletions, 450 inversions, 450 duplications, and 250 inter-chromosomal translocations, should be 4,674.</p><p>The original version was: “For the simulation datasets, we first simulated 3668 structural variations on chromosomes 1 and 2, including 2191 insertions, 1333 deletions, 450 inversions, 450 duplications, and 250 inter-chromosomal translocations, and reconstructed the reference genome GRCh38 with these SVs for the donor genome.”</p><p>The corrected version was: “For the simulation datasets, we first simulated <b>4674</b> structural variations on chromosomes 1 and 2, including 2191 insertions, 1333 deletions, 450 inversions, 450 duplications, and 250 inter-chromosomal translocations, and reconstructed the reference genome GRCh38 with these SVs for the donor genome”. The change was marked as bold. This correction does not affect the study’s results or conclusions.</p><p>2. In the <i>Funding</i> section, there contained redundant text, with the same grant details repeated in two separate paragraphs. We removed the duplicated paragraph and preserved the original content in the first paragraph.</p><p>The original version was: “This work has been supported by the National Key R&D Program of China (Grant number 2022YFF1202101, 2024YFC3406303, 2017YFC0907503), the National Natural Science Foundation of China (Grant number 62472120, 62331012), China Postdoctoral Science Foundation (Grant Number 2022M720965), and Heilongjiang Postdoctoral Foundation (Grant Number LBH-Z22174).</p><p><b>National Key Research and Development Program of China, 2024YFC3406303, 2022YFF1202101, 2017YFC0907503, National Natural Science Foundation of China, 62472120, 62331012, China Postdoctoral Science Foundation, 2022M720965, Heilongjiang Postdoctoral Science Foundation, LBH-Z22174”</b>.</p><p>The corrected version was: “This work has been supported by the National Key R&D Program of China (Grant number 2022YFF1202101, 2024YFC3406303, 2017YFC0907503), the National Natural Science Foundation of China (Grant number 62472120, 62331012), China Postdoctoral Science Foundation (Grant Number 2022M720965), and Heilongjiang Postdoctoral Foundation (Grant Number LBH-Z22174)”.</p><p>The deleted paragraph was marked as bold. This correction only removes the duplicated funding, and does not alter the funding sources or their attribution.</p><p>3. In the left portion of Fig. 2D, the proportion of simulated reads for alternative alleles to simulated reads for reference ","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"69 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145059288","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Diverse short tandem repeat sequences influence gene regulation in human populations","authors":"Aleksandra Mitina, Worrawat Engchuan, Brett Trost, Giovanna Pellecchia, Stephen W. Scherer, Ryan K. C. Yuen","doi":"10.1186/s13059-025-03754-9","DOIUrl":"https://doi.org/10.1186/s13059-025-03754-9","url":null,"abstract":"Short tandem repeat (STR) length is a known determinant of pathogenicity in a variety of human disorders. The repeat sequence itself can modulate disease severity and penetrance; however, the broader impact of STR sequence variation on gene expression in the general population remains poorly understood. Here, we analyze the sequence composition of STRs across two general population cohorts of unrelated individuals (n = 3,150) and report that ~ 7% of STRs exhibit sequence variability, with distinct patterns observed among different ethnic groups. These variable repeats are more prone to expansion and are frequently found in proximity to Alu elements. Notably, STRs with variable motifs are often found near splice junctions of genes involved in brain and neuronal functions. This is supported by the differential expression of genes associated with neuron and cellular projection functions, driven by the presence of distinct STR sequences. Our findings underscore the previously unrecognized role of STR sequence variability in modulating gene expression and contributing to human phenotypic diversity.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"130 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145035110","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Author Correction: Engineering novel CRISPRi repressors for highly efficient mammalian gene regulation","authors":"Andrew Kristof, Krithika Karunakaran, Christopher Allen, Paula Mizote, Sophie Briggs, Zixin Jian, Patrick Nash, John Blazeck","doi":"10.1186/s13059-025-03746-9","DOIUrl":"https://doi.org/10.1186/s13059-025-03746-9","url":null,"abstract":"<p><b>Correction: Genome Biology 26, 164 (2025)</b></p><p><b>https://doi.org/10.1186/s13059-025-03640-4</b></p><br/><p>Following publication of the original article, “Engineering novel CRISPRi repressors for highly efficient mammalian gene regulation” [1], authors have added an additional citation to a previous work [2] that demonstrates that dCas9-Zim3-MECP2 leads to efficient and long-term epigenetic silencing.</p><p>Additionally, the authors have made the following changes to the text to reflect the contributions of the previous work.</p><p><b>Figure changes:</b></p><p>(1) The bar colors in <b>Fig. 1D and 1F</b> have been fixed to show that dCas9-ZIM3-MeCP2 is a previously published CRISPRi system.</p><p>Original:</p><figure><picture><source srcset=\"//media.springernature.com/lw685/springer-static/image/art%3A10.1186%2Fs13059-025-03746-9/MediaObjects/13059_2025_3746_Figa_HTML.png?as=webp\" type=\"image/webp\"/><img alt=\"figure a\" aria-describedby=\"Figa\" height=\"713\" loading=\"lazy\" src=\"//media.springernature.com/lw685/springer-static/image/art%3A10.1186%2Fs13059-025-03746-9/MediaObjects/13059_2025_3746_Figa_HTML.png\" width=\"685\"/></picture></figure><p>Corrected:</p><figure><picture><source srcset=\"//media.springernature.com/lw685/springer-static/image/art%3A10.1186%2Fs13059-025-03746-9/MediaObjects/13059_2025_3746_Figb_HTML.png?as=webp\" type=\"image/webp\"/><img alt=\"figure b\" aria-describedby=\"Figb\" height=\"709\" loading=\"lazy\" src=\"//media.springernature.com/lw685/springer-static/image/art%3A10.1186%2Fs13059-025-03746-9/MediaObjects/13059_2025_3746_Figb_HTML.png\" width=\"685\"/></picture></figure><p><b>(2) Supplementary Figure S3</b> and its caption have been updated to change the color of the previously characterized dCas9-ZIM3-MeCP2 to be gray such that it is different than the three novel bipartite variants to prevent possible confusion about its novelty.</p><p>Original:</p><figure><picture><source srcset=\"//media.springernature.com/lw685/springer-static/image/art%3A10.1186%2Fs13059-025-03746-9/MediaObjects/13059_2025_3746_Figc_HTML.png?as=webp\" type=\"image/webp\"/><img alt=\"figure c\" aria-describedby=\"Figc\" height=\"270\" loading=\"lazy\" src=\"//media.springernature.com/lw685/springer-static/image/art%3A10.1186%2Fs13059-025-03746-9/MediaObjects/13059_2025_3746_Figc_HTML.png\" width=\"685\"/></picture></figure><p><b>Supplementary Figure S3</b>. Gene silencing achieved by improved bipartite repressor domains. (<b>A</b>) Comparison of top-performing prior CRISPRi platforms and novel bipartite repressor variants in HEK293T cells. Indicated dCas9-repressor fusions and eGFP reporter construct (with alternative sgRNA −313(T) targeting the SV40 promoter) were co-transfected and samples were assayed 72 h later using flow cytometry. Wild type (WT) cells indicate level of complete eGFP silencing. (<b>B</b>) Histograms showing the distribution of eGFP fluorescence for current “gold standards” and one novel variant, KOX1(KRAB)-MeCP2(t) compared to cells expressing o","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"33 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145035111","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Single-cell atlas in the living fossil Yangtze sturgeon provides insight into the evolution of fish","authors":"Yeyu Chen, Xiaoyun Wu, Jiansheng Lai, Pengcheng Li, Ya Liu, Zhao Liu, Qiaolin Zou, Luyun Ni, Mingjiang Song, Feiyang Li, Quan Gong","doi":"10.1186/s13059-025-03764-7","DOIUrl":"https://doi.org/10.1186/s13059-025-03764-7","url":null,"abstract":"Fish are the largest group of vertebrates. Studying the characteristics, functions, and interactions of different fish cells is important for understanding their roles in disease and evolution. However, most single cell RNA-seq studies in fish are restricted to a few specific organs, leaving a comprehensive cell landscape that aims to characterize the heterogeneity and connections among body-wide organs largely unexplored. We construct a single-cell atlas from the Yangtze sturgeon, Acipenser dabryanus, containing 82,401 high-quality cells and identify 72 major cell types. We compare differentially expressed genes among enterocytes in each part of the intestines and reveal the differences in absorption function of pyloric caecum, duodenum, spiral intestine, and rectum. Best4/Otop2 cells, newly identified in human, are also found in the intestines of sturgeon, indicating that these cells originated in an ancient period. We confirm the status of Müller glia as resident stem cells in fish nervous systems. We also characterize the different immune function between mucosa- and systemic-associated tissues. We detect several unexpected types of cells in Yangtze sturgeon, confirming that sturgeon is basal to teleosts. Cross-species analysis further indicates that sturgeon might occupy an ancient evolutionary position bridging the transition from cartilaginous to bony fish. In addition, novel cell markers, transcription factors, and intercellular communications are identified and found to be associated with the biological functions of specific types of cells. We generate the cellular landscape of an ancient fish and provide a valuable resource for revealing the cellular heterogeneity and biology of vertebrates.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"44 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145025697","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"MAGdb: a comprehensive high quality MAGs repository for exploring microbial metagenome-assemble genomes","authors":"Guo Ye, Hao Hong, Ting Li, Jin Li, Jia-Qi Wu, Shuai Jiang, Zhi-Tong Meng, He-Tian Yuan, Wen Xue, Ai-Ling Li, Tao Zhou, Ting-Ting Li, Tao Li","doi":"10.1186/s13059-025-03711-6","DOIUrl":"https://doi.org/10.1186/s13059-025-03711-6","url":null,"abstract":"Metagenomic analyses of microbial communities have unveiled a substantial level of interspecies and intraspecies genetic diversity by reconstructing metagenome-assembled genomes (MAGs). The MAG database (MAGdb) boasts an impressive collection of 74 representative research papers, spanning clinical, environmental, and animal categories and comprising 13,702 paired-end run accessions of metagenomic sequencing and 99,672 high quality MAGs with manually curated metadata. MAGdb provides a user-friendly interface that users can browse, search, and download MAGs and their corresponding metadata information. It represents a valuable resource for researchers in discovering potential novel microbial lineages and understanding their ecological roles. MAGdb is publicly available at https://magdb.nanhulab.ac.cn/ .","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"53 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145025698","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}