{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,17]],"date-time":"2026-05-17T07:58:58Z","timestamp":1779004738195,"version":"3.51.4"},"reference-count":39,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2024,3,27]],"date-time":"2024-03-27T00:00:00Z","timestamp":1711497600000},"content-version":"vor","delay-in-days":86,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Taishan Scholars Program of Shandong Province"},{"name":"Shandong Provincial Science and Technology Innovation Fund"},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Taishan Scholars Program of Shandong Province"},{"name":"Shandong Provincial Science and Technology Innovation Fund"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,3,27]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Pangenomes, capturing the genetic diversity of a species or genus, are essential to understanding the ecology, pathobiology and evolutionary mechanisms of fungi that cause infection in crops and humans. However, fungal pangenome databases remain unavailable. Here, we report the first fungal pangenome database, specifically for Fusarium oxysporum species complex (FOSC), a group of cross-kingdom pathogens causing devastating vascular wilt to over 100 plant species and life-threatening fusariosis to immunocompromised humans. The F. oxysporum Pangenome Database (FoPGDB) is a comprehensive resource integrating 35 high-quality FOSC genomes, coupled with robust analytical tools. FoPGDB allows for both gene-based and graph-based exploration of the F. oxysporum pangenome. It also curates a large repository of putative effector sequences, crucial for understanding the mechanisms of FOSC pathogenicity. With an assortment of functionalities including gene search, genomic variant exploration and tools for functional enrichment, FoPGDB provides a platform for in-depth investigations of the genetic diversity and adaptability of F. oxysporum. The modular and user-friendly interface ensures efficient data access and interpretation. FoPGDB promises to be a valuable resource for F. oxysporum research, contributing to our understanding of this pathogen\u2019s pangenomic landscape and aiding in the development of novel disease management strategies.<\/jats:p>\n               <jats:p>Database URL: http:\/\/www.fopgdb.site<\/jats:p>","DOI":"10.1093\/database\/baae017","type":"journal-article","created":{"date-parts":[[2024,3,27]],"date-time":"2024-03-27T19:57:22Z","timestamp":1711569442000},"source":"Crossref","is-referenced-by-count":11,"title":["FoPGDB: a pangenome database of <i>Fusarium oxysporum<\/i>, a cross-kingdom fungal pathogen"],"prefix":"10.1093","volume":"2024","author":[{"given":"Tan","family":"Meng","sequence":"first","affiliation":[{"name":"Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang , Weifang, Shandong 261325, China"},{"name":"Department of Computer Science, The University of Hong Kong , Hong Kong 999077, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hanqing","family":"Jiao","sequence":"additional","affiliation":[{"name":"Department of Computer Science, The University of Hong Kong , Hong Kong 999077, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yi","family":"Zhang","sequence":"additional","affiliation":[{"name":"Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang , Weifang, Shandong 261325, China"},{"name":"College of Information and Electrical Engineering, China Agricultural University , Haidian District, Beijing 100083, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yi","family":"Zhou","sequence":"additional","affiliation":[{"name":"Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang , Weifang, Shandong 261325, China"},{"name":"College of Information and Electrical Engineering, China Agricultural University , Haidian District, Beijing 100083, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shaoying","family":"Chen","sequence":"additional","affiliation":[{"name":"Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang , Weifang, Shandong 261325, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xinrui","family":"Wang","sequence":"additional","affiliation":[{"name":"Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang , Weifang, Shandong 261325, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bowen","family":"Yang","sequence":"additional","affiliation":[{"name":"Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang , Weifang, Shandong 261325, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jie","family":"Sun","sequence":"additional","affiliation":[{"name":"Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang , Weifang, Shandong 261325, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xin","family":"Geng","sequence":"additional","affiliation":[{"name":"Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang , Weifang, Shandong 261325, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dilay Hazal","family":"Ayhan","sequence":"additional","affiliation":[{"name":"Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang , Weifang, Shandong 261325, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6100-3481","authenticated-orcid":false,"given":"Li","family":"Guo","sequence":"additional","affiliation":[{"name":"Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang , Weifang, Shandong 261325, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2024,3,27]]},"reference":[{"key":"2024062912190054100_R1","doi-asserted-by":"crossref","first-page":"414","DOI":"10.1111\/j.1364-3703.2011.00783.x","article-title":"The top 10 fungal pathogens in molecular plant pathology","volume":"13","author":"Dean","year":"2012","journal-title":"Mol. Plant Pathol."},{"key":"2024062912190054100_R2","doi-asserted-by":"crossref","first-page":"399","DOI":"10.1146\/annurev-micro-092412-155650","article-title":"Fusarium pathogenomics","volume":"67","author":"Ma","year":"2013","journal-title":"Annu. Rev. Microbiol."},{"key":"2024062912190054100_R3","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1146\/annurev-phyto-080615-095919","article-title":"Fusarium oxysporum and the Fusarium Wilt Syndrome","volume":"55","author":"Gordon","year":"2017","journal-title":"Annu. Rev. Phytopathol."},{"key":"2024062912190054100_R4","doi-asserted-by":"crossref","first-page":"695","DOI":"10.1128\/CMR.00014-07","article-title":"Fusarium infections in immunocompromised patients","volume":"20","author":"Nucci","year":"2007","journal-title":"Clin. Microbiol. Rev."},{"key":"2024062912190054100_R5","doi-asserted-by":"crossref","first-page":"1491","DOI":"10.1007\/s10096-013-1924-7","article-title":"Fusariosis, a complex infection caused by a high diversity of fungal species refractory to treatment","volume":"32","author":"Guarro","year":"2013","journal-title":"Eur. J. Clin. Microbiol. Infect. Dis."},{"key":"2024062912190054100_R6","doi-asserted-by":"crossref","first-page":"243","DOI":"10.1038\/s41576-020-0210-7","article-title":"Pan-genomics in the human genome era","volume":"21","author":"Sherman","year":"2020","journal-title":"Nat. Rev. Genet."},{"key":"2024062912190054100_R7","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.2220570120","article-title":"Hiding in plain sight: genome-wide recombination and a dynamic accessory genome drive diversity in Fusarium oxysporum f.sp. ciceris","volume":"120","author":"Fayyaz","year":"2023","journal-title":"Proc. Natl. Acad. 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