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.

Figure 1.

Shows the change in Ensembl Bacteria's collection, aggregated by our ten largest represented phylums, between releases 48 and 49. Component A shows the overall change in genome numbers in each phylum with over 15,000 genomes coming from three phylums. Component B demonstrates that overall family coverage within phylums has improved irrespective of the removal of genomes. Component C shows an increase in genomes without a known family with the majority occurring in Proteobacteria.

Figure 2.

EPO multiple genome alignment visualization of chromosome 1 in three rice genomes: Oryza sativa indica Group (top), Oryza sativa japonica Group (middle) and Oryza glaberrima (bottom). Orange discontinuous blocks represent the areas of alignment across all three genomes. Each genome displays its genes and can be used to identify regions of uniqueness in each genome and identify potential areas of mis-assembly or mis-annotation. This alignment can be browsed at http://plants.ensembl.org/Oryza_nivara/Location/Compara_Alignments/Image?align = 9910;db = core;r = 1:586653–632276.

Figure 3.

An AlphaFold 3D prediction for the Arabidopsis thaliana protein Q00958 (LFY: AT5G61850.1) displayed as a Richardson model using Mol*. The central panel annotates the model with regions of high confidence (blue) to low confidence (orange) with its protein sequence displayed above. The right hand panel enables highlighting of one or more exons, variants and protein features which are controlled by clicking on the eye icon. Variants can be turned on/off according to how deleterious or tolerated they are or individually. Only variants resulting in protein changes with SIFT scores are made available for display.