Ensembl 2022

Abstract

Ensembl (https://www.ensembl.org) is unique in its flexible infrastructure for access to genomic data and annotation. It has been designed to efficiently deliver annotation at scale for all eukaryotic life, and it also provides deep comprehensive annotation for key species. Genomes representing a greater diversity of species are increasingly being sequenced. In response, we have focussed our recent efforts on expediting the annotation of new assemblies. Here, we report the release of the greatest annual number of newly annotated genomes in the history of Ensembl via our dedicated Ensembl Rapid Release platform (http://rapid.ensembl.org). We have also developed a new method to generate comparative analyses at scale for these assemblies and, for the first time, we have annotated non-vertebrate eukaryotes. Meanwhile, we continually improve, extend and update the annotation for our high-value reference vertebrate genomes and report the details here. We have a range of specific software tools for specific tasks, such as the Ensembl Variant Effect Predictor (VEP) and the newly developed interface for the Variant Recoder. All Ensembl data, software and tools are freely available for download and are accessible programmatically.

Figure 1.

Homology annotation pipeline. (A) For each query genome, the pipeline starts with the identification of the correct genome representative set based on the query genome taxonomy. Then the query genome and the representative genomes are compared using Diamond-Blast. The Diamond-Blast output is analysed to identify reciprocal best hit (RBH) or best hit (BH) if no RBH is found against the query genome or representative genomes. The RBH and BH homology relationships are then stored in a per species Compara database. These data are then displayed in the homology view of the Rapid Release platform. (B) List of representative genomes shared by all the representative sets. (C) The set of representative genomes used for the bony fish (actinopterygii) are here in larger font. Their selection has been based on community usage and annotation quality. The red and blue branches define clusters of actinopterygii subclades identified by their branch length. At least one representative per subclade has been selected. (D) The sets of representative genomes that are currently available in Ensembl.

Figure 2.

Entity viewer with transcript filtering and sorting. Screenshot of entity viewer showing protein coding transcripts available for BRCA2 (ENSG00000139618.17, GRCh38), ordered according to the number of exons. Information about the selected gene is displayed in the right-hand menu with cross references available by clicking on ‘External references’. Multiple functions are available from the right-hand control strip including a gene search (magnifying glass icon), recently visited genes (bookmark icon) and sequence download (download icon). Additional information about each transcript can be accessed from the ‘More information’ link, and sequence data for a single transcript can be accessed from the ‘Download’ link.