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Whole genome duplication (WGD) is one of the sources of duplicated genes. It can provide raw materials for natural selection by increasing the flexibility and complexity of the genome. WGDs are the driving force for the evolution of vertebrates and contribute greatly to their species diversity, especially in fish species with complicated WGD patterns. Here, we constructed the DupScan database (https:\/\/dupscan.sysumeg.com\/) by integrating 106 chromosomal-level genomes, which can analyze and visualize synteny at both the gene and genome scales, visualize the Ka, Ks, and 4DTV values, and browse genomes. DupScan was used to perform functional adaptation for the intricate WGD investigation based on synteny matching. DupScan supports the analysis of five WGD rounds (R): VGD2 (vertebrate genome duplication 2), Ars3R (Acipenser-ruthenus-specific 3R), Pss3R (Polyodon-spathula-specific 3R), Ts3R (teleost-specific duplication 3R), Ss4R (salmonid-specific 4R), and Cs4R (carp-specific 4R). DupScan serves as one-stop analysis platform for synteny and WGD research in which users can analyze and predict synteny and WGD patterns across 106 species of whole genome sequences. This further aided us in elucidating genome evolutionary patterns across over 60,000 vertebrate species with synteny and WGD events.<\/jats:p>","DOI":"10.1093\/nar\/gkac718","type":"journal-article","created":{"date-parts":[[2022,8,26]],"date-time":"2022-08-26T17:08:19Z","timestamp":1661533699000},"page":"D906-D912","source":"Crossref","is-referenced-by-count":7,"title":["DupScan: predicting and visualizing vertebrate genome duplication database"],"prefix":"10.1093","volume":"51","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3966-8812","authenticated-orcid":false,"given":"Jianguo","family":"Lu","sequence":"first","affiliation":[{"name":"School of Marine Sciences, Sun Yat-sen University , Zhuhai \u00a0519082,\u00a0 China"},{"name":"Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) , Zhuhai \u00a0519080,\u00a0 China"},{"name":"Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering , Guangzhou \u00a0510275,\u00a0 China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Peilin","family":"Huang","sequence":"additional","affiliation":[{"name":"School of Marine Sciences, Sun Yat-sen University , Zhuhai \u00a0519082,\u00a0 China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jialiang","family":"Sun","sequence":"additional","affiliation":[{"name":"College of Computer Science, Nankai University , Tianjin \u00a0300350,\u00a0 China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5516-0157","authenticated-orcid":false,"given":"Jian","family":"Liu","sequence":"additional","affiliation":[{"name":"College of Computer Science, Nankai University , Tianjin \u00a0300350,\u00a0 China"},{"name":"Centre for Bioinformatics and Intelligent Medicine, Nankai University , Tianjin \u00a0300350,\u00a0 China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2022,8,26]]},"reference":[{"key":"2023010804272126100_B1","doi-asserted-by":"crossref","first-page":"1151","DOI":"10.1126\/science.290.5494.1151","article-title":"The evolutionary fate and consequences of duplicate genes","volume":"290","author":"Lynch","year":"2000","journal-title":"Science"},{"key":"2023010804272126100_B2","doi-asserted-by":"crossref","first-page":"938","DOI":"10.1038\/nrg2482","article-title":"Turning a hobby into a job: how duplicated genes find new functions","volume":"9","author":"Conant","year":"2008","journal-title":"Nat. Rev. Genet."},{"key":"2023010804272126100_B3","doi-asserted-by":"crossref","first-page":"349","DOI":"10.1038\/nature05984","article-title":"Positive darwinian selection at the imprinted MEDEA locus in plants","volume":"448","author":"Spillane","year":"2007","journal-title":"Nature"},{"key":"2023010804272126100_B4","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1016\/j.tig.2021.06.016","article-title":"Retention of duplicated genes in evolution","volume":"38","author":"Kuzmin","year":"2022","journal-title":"Trends Genet."},{"key":"2023010804272126100_B5","doi-asserted-by":"crossref","first-page":"411","DOI":"10.1038\/nrg.2017.26","article-title":"The evolutionary significance of polyploidy","volume":"18","author":"Van\u00a0de\u00a0Peer","year":"2017","journal-title":"Nat. Rev. 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U.S.A."},{"key":"2023010804272126100_B33","doi-asserted-by":"crossref","first-page":"eaav0547","DOI":"10.1126\/sciadv.aav0547","article-title":"De novo assembly of the goldfish (Carassius auratus) genome and the evolution of genes after whole-genome duplication","volume":"5","author":"Chen","year":"2019","journal-title":"Sci. Adv."}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/51\/D1\/D906\/48440980\/gkac718.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/51\/D1\/D906\/48440980\/gkac718.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,8]],"date-time":"2023-01-08T04:28:34Z","timestamp":1673152114000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/51\/D1\/D906\/6677325"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,8,26]]},"references-count":33,"journal-issue":{"issue":"D1","published-online":{"date-parts":[[2022,8,26]]},"published-print":{"date-parts":[[2023,1,6]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkac718","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2023,1,6]]},"published":{"date-parts":[[2022,8,26]]}}}