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

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.

The 2022Nucleic Acids Researchdatabase issue and the online molecular biology database collection

“…A new interface is being implemented after researching user interaction patterns, and non-vertebrate genomes are also included for the first time as the database continues on the path to merger with Ensembl genomes. The paper on the latter ( 70 ) reports the largest content increase yet seen including almost 500 new fungal genomes. Other interesting developments include proteome-based removal of redundancy in hosted bacterial genomes, a move to better support pangenomes and inclusion of AlphaFold models for Arabidopsis.…”

Reconstruction of hundreds of reference ancestral genomes across the eukaryotic kingdom

“…Genes and gene trees were downloaded from in Ensembl v.92 56 , and Ensembl Plants v.41 57 . Ensembl v.92 gene trees were edited for poorly supported duplication nodes as previously described 58 , as part of the standard build procedure for the Genomicus synteny database.…”

The European Bioinformatics Institute (EMBL-EBI) in 2021

“…All EMBL-EBI data resources are continuously updated to ensure that they are relevant for the research community. EMBL-EBI databases that have had major updates are detailed in articles elsewhere in this issue of Nucleic Acids Research and include Ensembl ( 8 ), Ensembl Genomes ( 9 ), the Ensembl COVID-19 Browser ( 10 ), the European Variation Archive (EVA) ( 11 ), the European Genome-phenome Archive (EGA) ( 12 ), Expression Atlas ( 13 ), Complex Portal ( 14 ), IntAct ( 15 ), Reactome ( 16 ), and PRIDE ( 17 ). Here, we highlight some of the major developments that have been carried out over the last year in a number of other resources.…”