Ensembl Genomes 2020-enabling non-vertebrate genomic research

Abstract

Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context of the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent set of interfaces to genomic data across the tree of life, including reference genome sequence, gene models, transcriptional data, genetic variation and comparative analysis. Data may be accessed via our website, online tools platform and programmatic interfaces, with updates made four times per year (in synchrony with Ensembl). Here, we provide an overview of Ensembl Genomes, with a focus on recent developments. These include the continued growth, more robust and reproducible sets of orthologues and paralogues, and enriched views of gene expression and gene function in plants. Finally, we report on our continued deeper integration with the Ensembl project, which forms a key part of our future strategy for dealing with the increasing quantity of available genome-scale data across the tree of life.

Figure 1.

Baseline expression of barley gene HORVU2Hr1G092290, available as ‘Gene expression’ on the left menu. This feature is currently supported for the following plant species: Arabidopsis thaliana, Brassica rapa, Brachypodium distachyon, Hordeum vulgare, Glycine max, Oryza sativa, Populus trichocarpa, Setaria italica, Solanum tuberosum, Sorghum bicolor, Triticum aestivum and Zea mays.

Figure 2.

Wheat gene TraesCS1B02G195200 (phospholipase D) is annotated as an enzyme involved in choline biosynthesis. This diagram is available as ‘Pathway’ on the left menu. This is an orthology-based projection from rice gene OsPLDalpha1, which was curated from the literature at the Plant Reactome database.