Ensembl Genomes 2022: an expanding genome resource for non-vertebrates

Andrew Yates(European Bioinformatics Institute), James E. Allen(European Bioinformatics Institute), Ridwan Amode(European Bioinformatics Institute), Andrey G Azov(European Bioinformatics Institute), Matthieu Barba(European Bioinformatics Institute), Andrés Becerra(European Bioinformatics Institute), Jyothish Bhai(European Bioinformatics Institute), Lahcen Campbell(European Bioinformatics Institute), Manuel Carbajo Martinez(European Bioinformatics Institute), Marc Chakiachvili(European Bioinformatics Institute), Kapeel Chougule(Cold Spring Harbor Laboratory), Mikkel Christensen(European Bioinformatics Institute), Bruno Contreras‐Moreira(European Bioinformatics Institute), Alayne Cuzick(Rothamsted Research), Luca Da Rin Fioretto(European Bioinformatics Institute), Paul A. Davis(European Bioinformatics Institute), Nishadi De Silva(European Bioinformatics Institute), Stavros Diamantakis(European Bioinformatics Institute), Sarah Dyer(European Bioinformatics Institute), Justin Elser(Oregon State University), Carla Valeria Filippi(European Bioinformatics Institute), Astrid Gall(European Bioinformatics Institute), Dionysios Grigoriadis(European Bioinformatics Institute), Cristina Guijarro-Clarke(European Bioinformatics Institute), Parul Gupta(Oregon State University), K. E. Hammond‐Kosack(Rothamsted Research), Kevin Howe(European Bioinformatics Institute), Pankaj Jaiswal(Oregon State University), Vinay Kaikala(European Bioinformatics Institute), Vivek Kumar(Cold Spring Harbor Laboratory), Sunita Kumari(Cold Spring Harbor Laboratory), Nicholas Langridge(European Bioinformatics Institute), Anh Tuấn Lê(European Bioinformatics Institute), Manuel Luypaert(European Bioinformatics Institute), G. Maslen(European Bioinformatics Institute), Thomas Maurel(European Bioinformatics Institute), Benjamin Moore(European Bioinformatics Institute), Matthieu Muffato(European Bioinformatics Institute), Aleena Mushtaq(European Bioinformatics Institute), Guy Naamati(European Bioinformatics Institute), Sushma Naithani(Oregon State University), Andrew Olson(Cold Spring Harbor Laboratory), Anne Parker(European Bioinformatics Institute), Michael Paulini(European Bioinformatics Institute), Helder Pedro(European Bioinformatics Institute), Emily Perry(European Bioinformatics Institute), Justin Preece(Oregon State University), Mark Quinton-Tulloch(European Bioinformatics Institute), Faye H. Rodgers(Wellcome Sanger Institute), Marc Rosello(European Bioinformatics Institute), Magali Ruffier(European Bioinformatics Institute), James Seager(Rothamsted Research), Vasily Sitnik(European Bioinformatics Institute), Michał Szpak(European Bioinformatics Institute), John Tate(European Bioinformatics Institute), Marcela K Tello-Ruiz(Cold Spring Harbor Laboratory), Stephen J. Trevanion(European Bioinformatics Institute), Martin Urban(Rothamsted Research), Doreen Ware(Agricultural Research Service), Sharon Wei(Cold Spring Harbor Laboratory), Gary W. Williams(European Bioinformatics Institute), Andrea Winterbottom(European Bioinformatics Institute), Magdalena Zarowiecki(European Bioinformatics Institute), ROBERT FINN(European Bioinformatics Institute), Paul Flicek(European Bioinformatics Institute)
Nucleic Acids Research
November 10, 2021
10.1093/nar/gkab1007
Cited by 441Open Access
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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.

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