Ensembl Genomes 2022: an expanding genome resource for non-vertebrates
Author:
Yates Andrew D1ORCID, Allen James1, Amode Ridwan M1, Azov Andrey G1, Barba Matthieu1, Becerra Andrés1, Bhai Jyothish1, Campbell Lahcen I1, Carbajo Martinez Manuel1, Chakiachvili Marc1, Chougule Kapeel2, Christensen Mikkel1, Contreras-Moreira Bruno1, Cuzick Alayne3ORCID, Da Rin Fioretto Luca1, Davis Paul1ORCID, De Silva Nishadi H1ORCID, Diamantakis Stavros1, Dyer Sarah1, Elser Justin4, Filippi Carla V156, Gall Astrid1, Grigoriadis Dionysios1, Guijarro-Clarke Cristina1, Gupta Parul4, Hammond-Kosack Kim E3ORCID, Howe Kevin L1ORCID, Jaiswal Pankaj4ORCID, Kaikala Vinay1, Kumar Vivek2, Kumari Sunita2, Langridge Nick1, Le Tuan1, Luypaert Manuel1, Maslen Gareth L1, Maurel Thomas1, Moore Benjamin1, Muffato Matthieu1, Mushtaq Aleena1, Naamati Guy1, Naithani Sushma4ORCID, Olson Andrew2, Parker Anne1, Paulini Michael1, Pedro Helder1, Perry Emily1ORCID, Preece Justin4, Quinton-Tulloch Mark1, Rodgers Faye7, Rosello Marc1, Ruffier Magali1ORCID, Seager James3ORCID, Sitnik Vasily1, Szpak Michal1, Tate John1, Tello-Ruiz Marcela K2, Trevanion Stephen J1, Urban Martin3ORCID, Ware Doreen28, Wei Sharon2, Williams Gary1, Winterbottom Andrea1, Zarowiecki Magdalena1, Finn Robert D1ORCID, Flicek Paul1ORCID
Affiliation:
1. European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK 2. Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA 3. Rothamsted Research, Department of Biointeractions and Crop Protection, Harpenden, Hertfordshire AL5 2JQ, UK 4. Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA 5. Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA); Instituto de Agrobiotecnología y Biología Molecular (IABIMO), INTA-CONICET Nicolas Repetto y Los Reseros s/n (1686), Hurlingham, Buenos Aires, Argentina 6. Consejo Nacional de Investigaciones Científicas y Técnicas–CONICET, Ciudad Autónoma de Buenos Aires, Argentina 7. Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK 8. USDA ARS NAA Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, Ithaca, NY 14853, USA
Abstract
Abstract
Ensembl Genomes (https://www.ensemblgenomes.org) provides access to non-vertebrate genomes and analysis complementing vertebrate resources developed by the Ensembl project (https://www.ensembl.org). The two resources collectively present genome annotation through a consistent set of interfaces spanning the tree of life presenting genome sequence, annotation, variation, transcriptomic data and comparative analysis. Here, we present our largest increase in plant, metazoan and fungal genomes since the project's inception creating one of the world's most comprehensive genomic resources and describe our efforts to reduce genome redundancy in our Bacteria portal. We detail our new efforts in gene annotation, our emerging support for pangenome analysis, our efforts to accelerate data dissemination through the Ensembl Rapid Release resource and our new AlphaFold visualization. Finally, we present details of our future plans including updates on our integration with Ensembl, and how we plan to improve our support for the microbial research community. Software and data are made available without restriction via our website, online tools platform and programmatic interfaces (available under an Apache 2.0 license). Data updates are synchronised with Ensembl's release cycle.
Funder
UK Biosciences and Biotechnology Research Council Wellcome Trust UK Medical Research Council National Science Foundation United States Department of Agriculture Bill and Melinda Gates Foundation ELIXIR European Molecular Biology Laboratory National Institutes of Health National Institute of Allergy and Infectious Diseases Department of Health and Human Services European Union's Horizon 2020 Research and Innovation Programme Wellcome Connecting Science Enabling Fund
Publisher
Oxford University Press (OUP)
Cited by
199 articles.
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