{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,7]],"date-time":"2026-04-07T16:41:27Z","timestamp":1775580087369,"version":"3.50.1"},"reference-count":29,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2021,11,8]],"date-time":"2021-11-08T00:00:00Z","timestamp":1636329600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003130","name":"Research Foundation Flanders","doi-asserted-by":"publisher","award":["I002819N"],"award-info":[{"award-number":["I002819N"]}],"id":[{"id":"10.13039\/501100003130","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004385","name":"Ghent University","doi-asserted-by":"publisher","award":["BOF24Y2019001901"],"award-info":[{"award-number":["BOF24Y2019001901"]}],"id":[{"id":"10.13039\/501100004385","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004727","name":"VIB","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004727","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,1,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>PLAZA is a platform for comparative, evolutionary, and functional plant genomics. It makes a broad set of genomes, data types and analysis tools available to researchers through a user-friendly website, an API, and bulk downloads. In this latest release of the PLAZA platform, we are integrating a record number of 134 high-quality plant genomes, split up over two instances: PLAZA Dicots 5.0 and PLAZA Monocots 5.0. This number of genomes corresponds with a massive expansion in the number of available species when compared to PLAZA 4.0, which offered access to 71 species, a 89% overall increase. The PLAZA 5.0 release contains information for 5 882 730 genes, and offers pre-computed gene families and phylogenetic trees for 5 274 684 protein-coding genes. This latest release also comes with a set of new and updated features: a new BED import functionality for the workbench, improved interactive visualizations for functional enrichments and genome-wide mapping of gene sets, and a fully redesigned and extended API. Taken together, this new version offers extended support for plant biologists working on different families within the green plant lineage and provides an efficient and versatile toolbox for plant genomics. All PLAZA releases are accessible from the portal website: https:\/\/bioinformatics.psb.ugent.be\/plaza\/.<\/jats:p>","DOI":"10.1093\/nar\/gkab1024","type":"journal-article","created":{"date-parts":[[2021,10,13]],"date-time":"2021-10-13T20:54:10Z","timestamp":1634158450000},"page":"D1468-D1474","source":"Crossref","is-referenced-by-count":234,"title":["PLAZA 5.0: extending the scope and power of comparative and functional genomics in plants"],"prefix":"10.1093","volume":"50","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1873-2563","authenticated-orcid":false,"given":"Michiel","family":"Van\u00a0Bel","sequence":"first","affiliation":[{"name":"Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium"},{"name":"VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium"}]},{"given":"Francesca","family":"Silvestri","sequence":"additional","affiliation":[{"name":"Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium"},{"name":"VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6622-6350","authenticated-orcid":false,"given":"Eric M","family":"Weitz","sequence":"additional","affiliation":[{"name":"Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7620-4657","authenticated-orcid":false,"given":"Lukasz","family":"Kreft","sequence":"additional","affiliation":[{"name":"Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawi\u0144skiego 5A 02-106 Warsaw, Poland"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6691-4233","authenticated-orcid":false,"given":"Alexander","family":"Botzki","sequence":"additional","affiliation":[{"name":"VIB Bioinformatics Core, 9052 Ghent, Belgium"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6565-5145","authenticated-orcid":false,"given":"Frederik","family":"Coppens","sequence":"additional","affiliation":[{"name":"Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium"},{"name":"VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4790-2725","authenticated-orcid":false,"given":"Klaas","family":"Vandepoele","sequence":"additional","affiliation":[{"name":"Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium"},{"name":"VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium"},{"name":"Bioinformatics Institute Ghent, Ghent University, Technologiepark 71, 9052 Ghent, Belgium"}]}],"member":"286","published-online":{"date-parts":[[2021,11,8]]},"reference":[{"key":"2022010507344389300_B1","doi-asserted-by":"crossref","first-page":"3718","DOI":"10.1105\/tpc.109.071506","article-title":"PLAZA: a comparative genomics resource to study gene and genome evolution in plants","volume":"21","author":"Proost","year":"2009","journal-title":"Plant Cell"},{"key":"2022010507344389300_B2","doi-asserted-by":"crossref","first-page":"590","DOI":"10.1104\/pp.111.189514","article-title":"Dissecting plant genomes with the PLAZA comparative genomics platform","volume":"158","author":"Van\u00a0Bel","year":"2012","journal-title":"Plant Physiol."},{"key":"2022010507344389300_B3","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1270\/jsbbs.20146","article-title":"Chromosome-level de novo genome assemblies of over 100 plant species","volume":"71","author":"Shirasawa","year":"2021","journal-title":"Breed Sci"},{"key":"2022010507344389300_B4","doi-asserted-by":"crossref","first-page":"700","DOI":"10.1016\/j.tplants.2019.05.003","article-title":"Tools and strategies for long-read sequencing and de novo assembly of plant genomes","volume":"24","author":"Jung","year":"2019","journal-title":"Trends Plant Sci."},{"key":"2022010507344389300_B5","doi-asserted-by":"crossref","first-page":"D1464","DOI":"10.1093\/nar\/gkaa1068","article-title":"GreenPhylDB v5: a comparative pangenomic database for plant genomes","volume":"49","author":"Valentin","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"2022010507344389300_B6","first-page":"D682","article-title":"Ensembl 2020","volume":"48","author":"Yates","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"2022010507344389300_B7","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":"2022010507344389300_B8","doi-asserted-by":"crossref","first-page":"1513","DOI":"10.1093\/bib\/bby019","article-title":"Interactive and coordinated visualization approaches for biological data analysis","volume":"20","author":"Cruz","year":"2019","journal-title":"Brief. 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