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Together, the two resources provide a consistent set of interfaces to genomic data across the tree of life, including reference genome sequence, gene models, transcriptional data, genetic variation and comparative analysis. Data may be accessed via our website, online tools platform and programmatic interfaces, with updates made four times per year (in synchrony with Ensembl). Here, we provide an overview of Ensembl Genomes, with a focus on recent developments. These include the continued growth, more robust and reproducible sets of orthologues and paralogues, and enriched views of gene expression and gene function in plants. Finally, we report on our continued deeper integration with the Ensembl project, which forms a key part of our future strategy for dealing with the increasing quantity of available genome-scale data across the tree of life.<\/jats:p>","DOI":"10.1093\/nar\/gkz890","type":"journal-article","created":{"date-parts":[[2019,10,2]],"date-time":"2019-10-02T15:38:01Z","timestamp":1570030681000},"page":"D689-D695","source":"Crossref","is-referenced-by-count":431,"title":["Ensembl Genomes 2020\u2014enabling non-vertebrate genomic research"],"prefix":"10.1093","volume":"48","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1751-9226","authenticated-orcid":false,"given":"Kevin L","family":"Howe","sequence":"first","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK"}]},{"given":"Bruno","family":"Contreras-Moreira","sequence":"additional","affiliation":[{"name":"European Molecular Biology 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UK"}]},{"given":"Jorge","family":"Alvarez-Jarreta","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK"}]},{"given":"Matthieu","family":"Barba","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3991-0859","authenticated-orcid":false,"given":"Dan M","family":"Bolser","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK"}]},{"given":"Lahcen","family":"Cambell","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK"}]},{"given":"Manuel","family":"Carbajo","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK"}]},{"given":"Marc","family":"Chakiachvili","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK"}]},{"given":"Mikkel","family":"Christensen","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK"}]},{"given":"Carla","family":"Cummins","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK"}]},{"given":"Alayne","family":"Cuzick","sequence":"additional","affiliation":[{"name":"Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK"}]},{"given":"Paul","family":"Davis","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK"}]},{"given":"Silvie","family":"Fexova","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK"}]},{"given":"Astrid","family":"Gall","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK"}]},{"given":"Nancy","family":"George","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK"}]},{"given":"Laurent","family":"Gil","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK"}]},{"given":"Parul","family":"Gupta","sequence":"additional","affiliation":[{"name":"Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9699-485X","authenticated-orcid":false,"given":"Kim E","family":"Hammond-Kosack","sequence":"additional","affiliation":[{"name":"Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK"}]},{"given":"Erin","family":"Haskell","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8350-1235","authenticated-orcid":false,"given":"Sarah 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Campus, Hinxton, Cambridge CB10 1SD, UK"}]},{"given":"Daniel M","family":"Staines","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK"}]},{"given":"Joshua","family":"Stein","sequence":"additional","affiliation":[{"name":"Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA"}]},{"given":"Marcela K","family":"Tello-Ruiz","sequence":"additional","affiliation":[{"name":"Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA"}]},{"given":"Stephen J","family":"Trevanion","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK"}]},{"given":"Martin","family":"Urban","sequence":"additional","affiliation":[{"name":"Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, 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Holley Center for Agriculture and Health, Agricultural Research Service, Ithaca, NY 14853, USA"}]},{"given":"Gary","family":"Williams","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8886-4772","authenticated-orcid":false,"given":"Andrew D","family":"Yates","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3897-7955","authenticated-orcid":false,"given":"Paul","family":"Flicek","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK"}]}],"member":"286","published-online":{"date-parts":[[2019,10,10]]},"reference":[{"key":"2020010521381273000_B1","doi-asserted-by":"crossref","first-page":"D745","DOI":"10.1093\/nar\/gky1113","article-title":"Ensembl 2019","volume":"47","author":"Cunningham","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2020010521381273000_B2","doi-asserted-by":"crossref","first-page":"D48","DOI":"10.1093\/nar\/gkx1097","article-title":"The International Nucleotide Sequence Database Collaboration","volume":"46","author":"Karsch-Mizrachi","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2020010521381273000_B3","doi-asserted-by":"crossref","first-page":"D1181","DOI":"10.1093\/nar\/gkx1111","article-title":"Gramene 2018: unifying comparative genomics and pathway resources for plant research","volume":"46","author":"Tello-Ruiz","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2020010521381273000_B4","doi-asserted-by":"crossref","first-page":"D707","DOI":"10.1093\/nar\/gku1117","article-title":"VectorBase: an updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases","volume":"43","author":"Giraldo-Calderon","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"2020010521381273000_B5","doi-asserted-by":"crossref","first-page":"D869","DOI":"10.1093\/nar\/gkx998","article-title":"WormBase 2017: molting into a new stage","volume":"46","author":"Lee","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2020010521381273000_B6","doi-asserted-by":"crossref","first-page":"D506","DOI":"10.1093\/nar\/gky1049","article-title":"UniProt: a worldwide hub of protein knowledge","volume":"47","author":"UniProt","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2020010521381273000_B7","doi-asserted-by":"crossref","first-page":"1236","DOI":"10.1093\/bioinformatics\/btu031","article-title":"InterProScan 5: genome-scale protein function classification","volume":"30","author":"Jones","year":"2014","journal-title":"Bioinformatics"},{"key":"2020010521381273000_B8","doi-asserted-by":"crossref","first-page":"W589","DOI":"10.1093\/nar\/gkv350","article-title":"The BioMart community portal: an innovative alternative to large, centralized data repositories","volume":"43","author":"Smedley","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"2020010521381273000_B9","doi-asserted-by":"crossref","first-page":"eaar7191","DOI":"10.1126\/science.aar7191","article-title":"Shifting the limits in wheat research and breeding using a fully annotated reference genome","volume":"361","author":"International Wheat Genome Sequencing Consortium","year":"2018","journal-title":"Science"},{"key":"2020010521381273000_B10","doi-asserted-by":"crossref","first-page":"4.11.1","DOI":"10.1002\/0471250953.bi0411s48","article-title":"Genome annotation and curation using MAKER and MAKER-P","volume":"48","author":"Campbell","year":"2014","journal-title":"Curr. 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