{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,6]],"date-time":"2026-02-06T05:08:14Z","timestamp":1770354494060,"version":"3.49.0"},"reference-count":58,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2022,9,28]],"date-time":"2022-09-28T00:00:00Z","timestamp":1664323200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"National Key Research Program of China","award":["2020YFA0907001"],"award-info":[{"award-number":["2020YFA0907001"]}]},{"name":"Strategic Priority Research Program of the Chinese Academy of Sciences","award":["XDB38030400"],"award-info":[{"award-number":["XDB38030400"]}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32170669"],"award-info":[{"award-number":["32170669"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002858","name":"China Postdoctoral Science Foundation","doi-asserted-by":"publisher","award":["2021M693109"],"award-info":[{"award-number":["2021M693109"]}],"id":[{"id":"10.13039\/501100002858","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Specialized Research Assistant Program of the Chinese Academy of Sciences","award":["202044"],"award-info":[{"award-number":["202044"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,1,6]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Compared with conventional comparative genomics, the recent studies in pan-genomics have provided further insights into species genomic dynamics, taxonomy and identification, pathogenicity and environmental adaptation. To better understand genome characteristics of species of interest and to fully excavate key metabolic and resistant genes and their conservations and variations, here we present ProPan (https:\/\/ngdc.cncb.ac.cn\/propan), a public database covering 23 archaeal species and 1,481 bacterial species (in a total of 51,882 strains) for comprehensively profiling prokaryotic pan-genome dynamics. By analyzing and integrating these massive datasets, ProPan offers three major aspects for the pan-genome dynamics of the species of interest: 1) the evaluations of various species' characteristics and composition in pan-genome dynamics; 2) the visualization of map association, the functional annotation and presence\/absence variation for all contained species' gene clusters; 3) the typical characteristics of the environmental adaptation, including resistance genes prediction of 126 substances (biocide, antimicrobial drug and metal) and evaluation of 31 metabolic cycle processes. Besides, ProPan develops a very user-friendly interface, flexible retrieval and multi-level real-time statistical visualization. Taken together, ProPan will serve as a weighty resource for the studies of prokaryotic pan-genome dynamics, taxonomy and identification as well as environmental adaptation.<\/jats:p>","DOI":"10.1093\/nar\/gkac832","type":"journal-article","created":{"date-parts":[[2022,9,28]],"date-time":"2022-09-28T12:16:20Z","timestamp":1664367380000},"page":"D767-D776","source":"Crossref","is-referenced-by-count":20,"title":["ProPan: a comprehensive database for profiling prokaryotic pan-genome dynamics"],"prefix":"10.1093","volume":"51","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0918-5673","authenticated-orcid":false,"given":"Yadong","family":"Zhang","sequence":"first","affiliation":[{"name":"National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing \u00a0100101, China"},{"name":"CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing \u00a0100101, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8873-9229","authenticated-orcid":false,"given":"Hao","family":"Zhang","sequence":"additional","affiliation":[{"name":"National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing \u00a0100101, China"},{"name":"CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing \u00a0100101, China"},{"name":"University of Chinese Academy of Sciences , Beijing \u00a0100049, China"}]},{"given":"Zaichao","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Biology, The University of Western Ontario , London , Ontario \u00a0N6A 5B7, Canada"}]},{"given":"Qiheng","family":"Qian","sequence":"additional","affiliation":[{"name":"National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing \u00a0100101, China"},{"name":"CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing \u00a0100101, China"},{"name":"University of Chinese Academy of Sciences , Beijing \u00a0100049, China"}]},{"given":"Zhewen","family":"Zhang","sequence":"additional","affiliation":[{"name":"National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing \u00a0100101, China"},{"name":"CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing \u00a0100101, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2835-4340","authenticated-orcid":false,"given":"Jingfa","family":"Xiao","sequence":"additional","affiliation":[{"name":"National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing \u00a0100101, China"},{"name":"CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing \u00a0100101, China"},{"name":"University of Chinese Academy of Sciences , Beijing \u00a0100049, China"}]}],"member":"286","published-online":{"date-parts":[[2022,9,28]]},"reference":[{"key":"2023010804285869100_B1","doi-asserted-by":"crossref","first-page":"e92798","DOI":"10.1371\/journal.pone.0092798","article-title":"A reference pan-genome approach to comparative bacterial genomics: identification of novel epidemiological markers in pathogenic Campylobacter","volume":"9","author":"M\u00e9ric","year":"2014","journal-title":"PLoS One"},{"key":"2023010804285869100_B2","doi-asserted-by":"crossref","first-page":"13950","DOI":"10.1073\/pnas.0506758102","article-title":"Genome analysis of multiple pathogenic isolates of Streptococcusagalactiae: implications for the microbial \u201cpan-genome\u201d","volume":"102","author":"Tettelin","year":"2005","journal-title":"Proc. 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