OrthoDB v10: sampling the diversity of animal, plant, fungal, protist, bacterial and viral genomes for evolutionary and functional annotations of orthologs

Article Article scientifique Article OrthoDB v10: sampling the diversity of animal, plant, fungal, protist, bacterial and viral genomes for evolutionary and functional annotations of orthologs eng 2019 author Kriventseva Evgenia 640181 author Kouznetsov Dimitri 892598 author Tegenfeldt Fredrik 708726 author Manni Mose 848200 author Dias Renata De Oliveira 887504 author Simao Neto Felipe 731423 author Zdobnov Evgeny 636914 D807-D811 10.1093/nar/gky1053 30395283 0305-1048 OrthoDB (https://www.orthodb.org) provides evolutionary and functional annotations of orthologs. This update features a major scaling up of the resource coverage, sampling the genomic diversity of 1271 eukaryotes, 6013 prokaryotes and 6488 viruses. These include putative orthologs among 448 metazoan, 117 plant, 549 fungal, 148 protist, 5609 bacterial, and 404 archaeal genomes, picking up the best sequenced and annotated representatives for each species or operational taxonomic unit. OrthoDB relies on a concept of hierarchy of levels-of-orthology to enable more finely resolved gene orthologies for more closely related species. Since orthologs are the most likely candidates to retain functions of their ancestor gene, OrthoDB is aimed at narrowing down hypotheses about gene functions and enabling comparative evolutionary studies. Optional registered-user sessions allow on-line BUSCO assessments of gene set completeness and mapping of the uploaded data to OrthoDB to enable further interactive exploration of related annotations and generation of comparative charts. The accelerating expansion of genomics data continues to add valuable information, and OrthoDB strives to provide orthologs from the broadest coverage of species, as well as to extensively collate available functional annotations and to compute evolutionary annotations. The data can be browsed online, downloaded or assessed via REST API or SPARQL RDF compatible with both UniProt and Ensembl. Dewey 576.5 135 Département de médecine génétique et développement 21D false 493 Génomique Evolutionnaire Computationnelle 830 Nucleic Acids Research 47 a2b7b20b-0f43-4c45-bfa0-39d7d027040d Article (Published version) Public 30395283.pdf 1903911 application/pdf CC BY openAccess Faculté de médecine / Section de médecine fondamentale / Département de médecine génétique et développement

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OrthoDB v10: sampling the diversity of animal, plant, fungal, protist, bacterial and viral genomes for evolutionary and functional annotations of orthologs	Nucleic Acids Research			2019	493	743

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Dias, Renata De Oliveira