{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,15]],"date-time":"2026-05-15T21:31:54Z","timestamp":1778880714222,"version":"3.51.4"},"reference-count":35,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2020,11,25]],"date-time":"2020-11-25T00:00:00Z","timestamp":1606262400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Syngenta Seeds SAS"},{"name":"CGIAR Research Program, Roots, Tubers and Bananas"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,1,8]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Comparative genomics is the analysis of genomic relationships among different species and serves as a significant base for evolutionary and functional genomic studies. GreenPhylDB (https:\/\/www.greenphyl.org) is a database designed to facilitate the exploration of gene families and homologous relationships among plant genomes, including staple crops critically important for global food security. GreenPhylDB is available since 2007, after the release of the Arabidopsis thaliana and Oryza sativa genomes and has undergone multiple releases. With the number of plant genomes currently available, it becomes challenging to select a single reference for comparative genomics studies but there is still a lack of databases taking advantage several genomes by species for orthology detection. GreenPhylDBv5 introduces the concept of comparative pangenomics by harnessing multiple genome sequences by species. We created 19 pangenes and processed them with other species still relying on one genome. In total, 46 plant species were considered to build gene families and predict their homologous relationships through phylogenetic-based analyses. In addition, since the previous publication, we rejuvenated the website and included a new set of original tools including protein-domain combination, tree topologies searches and a section for users to store their own results in order to support community curation efforts.<\/jats:p>","DOI":"10.1093\/nar\/gkaa1068","type":"journal-article","created":{"date-parts":[[2020,10,22]],"date-time":"2020-10-22T11:10:40Z","timestamp":1603365040000},"page":"D1464-D1471","source":"Crossref","is-referenced-by-count":33,"title":["GreenPhylDB v5: a comparative pangenomic database for plant genomes"],"prefix":"10.1093","volume":"49","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0903-6811","authenticated-orcid":false,"given":"Valentin","family":"Guignon","sequence":"first","affiliation":[{"name":"Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier, France"},{"name":"French Institute of Bioinformatics (IFB)\u2014South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398 Montpellier France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Abdel","family":"Toure","sequence":"additional","affiliation":[{"name":"Syngenta Seeds SAS, 31790 Saint-Sauveur France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1849-1269","authenticated-orcid":false,"given":"Ga\u00ebtan","family":"Droc","sequence":"additional","affiliation":[{"name":"French Institute of Bioinformatics (IFB)\u2014South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398 Montpellier France"},{"name":"AGAP, Univ de Montpellier, CIRAD, INRAE, Montpellier SupAgro, F-34398 Montpellier, France"},{"name":"CIRAD, UMR AGAP, F-34398 Montpellier, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jean-Fran\u00e7ois","family":"Dufayard","sequence":"additional","affiliation":[{"name":"French Institute of Bioinformatics (IFB)\u2014South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398 Montpellier France"},{"name":"AGAP, Univ de Montpellier, CIRAD, INRAE, Montpellier SupAgro, F-34398 Montpellier, France"},{"name":"CIRAD, UMR AGAP, F-34398 Montpellier, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Matthieu","family":"Conte","sequence":"additional","affiliation":[{"name":"Syngenta Seeds SAS, 31790 Saint-Sauveur France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0284-1885","authenticated-orcid":false,"given":"Mathieu","family":"Rouard","sequence":"additional","affiliation":[{"name":"Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier, France"},{"name":"French Institute of Bioinformatics (IFB)\u2014South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398 Montpellier France"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2020,11,25]]},"reference":[{"key":"2021062317493521400_B1","doi-asserted-by":"crossref","first-page":"D1190","DOI":"10.1093\/nar\/gkx1002","article-title":"PLAZA 4.0: an integrative resource for functional, evolutionary and comparative plant genomics","volume":"46","author":"Van\u00a0Bel","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2021062317493521400_B2","doi-asserted-by":"crossref","first-page":"D1095","DOI":"10.1093\/nar\/gkq811","article-title":"GreenPhylDB v2.0: comparative and functional genomics in plants","volume":"39","author":"Rouard","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"2021062317493521400_B3","doi-asserted-by":"crossref","first-page":"D1178","DOI":"10.1093\/nar\/gkr944","article-title":"Phytozome: a comparative platform for green plant genomics","volume":"40","author":"Goodstein","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"2021062317493521400_B4","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1016\/j.cpb.2016.12.005","article-title":"Gramene database: navigating plant comparative genomics resources","volume":"7\u20138","author":"Gupta","year":"2016","journal-title":"Curr. 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