Ensembl Genomes 2016: more genomes, more complexity

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 programmatic and interactive interfaces to a rich range of data including reference sequence, gene models, transcriptional data, genetic variation and comparative analysis. This paper provides an update to the previous publications about the resource, with a focus on recent developments. These include the development of new analyses and views to represent polyploid genomes (of which bread wheat is the primary exemplar); and the continued up-scaling of the resource, which now includes over 23 000 bacterial genomes, 400 fungal genomes and 100 protist genomes, in addition to 55 genomes from invertebrate metazoa and 39 genomes from plants. This dramatic increase in the number of included genomes is one part of a broader effort to automate the integration of archival data (genome sequence, but also associated RNA sequence data and variant calls) within the context of reference genomes and make it available through the Ensembl user interfaces.

Figure 1.

Comparative genomics of bread wheat, as visualized in Ensembl Plants. Panel A shows the alignments of two homoeologous genes at the level of protein sequence. The selected gene is highlighted in red. Panel B shows these genes in the wider context of a gene tree, showing 1:1 orthology over 21 grass genomes including the 3 bread wheat genomes and the two sequenced diploid precursors.

Figure 2.

Whole genome alignment between the three bread wheat component genomes at a set of homoeologous loci. Inter-homoeologous variant calls and inter-variety polymorphisms are visible on tracks on each genome.