{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,16]],"date-time":"2026-07-16T04:14:31Z","timestamp":1784175271226,"version":"3.55.0"},"reference-count":38,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2024,4,18]],"date-time":"2024-04-18T00:00:00Z","timestamp":1713398400000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Research Foundation\u2014Flanders","award":["3G032219"],"award-info":[{"award-number":["3G032219"]}]},{"DOI":"10.13039\/501100004385","name":"Ghent University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004385","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,5,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Major improvements in sequencing technologies and genome sequence assembly have led to a huge increase in the number of available genome sequences. In turn, these genome sequences form an invaluable source for evolutionary, ecological, and comparative studies. One kind of analysis that has become routine is the search for traces of ancient polyploidy, particularly for plant genomes, where whole-genome duplication (WGD) is rampant.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Here, we present a major update of a previously developed tool wgd, namely wgd v2, to look for remnants of ancient polyploidy, or WGD. We implemented novel and improved previously developed tools to (a) construct KS age distributions for the whole-paranome (collection of all duplicated genes in a genome), (b) unravel intragenomic and intergenomic collinearity resulting from WGDs, (c) fit mixture models to age distributions of gene duplicates, (d) correct substitution rate variation for phylogenetic placement of WGDs, and (e) date ancient WGDs via phylogenetic dating of WGD-retained gene duplicates. The applicability and feasibility of wgd v2 for the identification and the relative and absolute dating of ancient WGDs is demonstrated using different plant genomes.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>wgd v2 is open source and available at https:\/\/github.com\/heche-psb\/wgd.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae272","type":"journal-article","created":{"date-parts":[[2024,4,18]],"date-time":"2024-04-18T02:14:15Z","timestamp":1713406455000},"source":"Crossref","is-referenced-by-count":51,"title":["wgd v2: a suite of tools to uncover and date ancient polyploidy and whole-genome duplication"],"prefix":"10.1093","volume":"40","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1173-6622","authenticated-orcid":false,"given":"Hengchi","family":"Chen","sequence":"first","affiliation":[{"name":"Department of Plant Biotechnology and Bioinformatics, Ghent University , Ghent 9052, Belgium"},{"name":"VIB Center for Plant Systems Biology, VIB , Ghent 9052, Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Arthur","family":"Zwaenepoel","sequence":"additional","affiliation":[{"name":"UMR 8198, Evo-Eco-Paleo, University of Lille, CNRS , Lille, F-59000, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yves","family":"Van de Peer","sequence":"additional","affiliation":[{"name":"Department of Plant Biotechnology and Bioinformatics, Ghent University , Ghent 9052, Belgium"},{"name":"VIB Center for Plant Systems Biology, VIB , Ghent 9052, Belgium"},{"name":"Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria , Pretoria 0028, South Africa"},{"name":"College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University , Nanjing 210095, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2024,4,17]]},"reference":[{"key":"2024050903012749600_btae272-B1","doi-asserted-by":"crossref","first-page":"1241089","DOI":"10.1126\/science.1241089","article-title":"The amborella genome and the evolution of flowering plants","volume":"342","author":"Albert","year":"2013","journal-title":"Science"},{"key":"2024050903012749600_btae272-B2","doi-asserted-by":"crossref","first-page":"1667","DOI":"10.1105\/tpc.021345","article-title":"Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes","volume":"16","author":"Blanc","year":"2004","journal-title":"Plant Cell"},{"key":"2024050903012749600_btae272-B3","doi-asserted-by":"crossref","first-page":"366","DOI":"10.1038\/s41592-021-01101-x","article-title":"Sensitive protein alignments at tree-of-life scale using DIAMOND","volume":"18","author":"Buchfink","year":"2021","journal-title":"Nat 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