Ensembl 2023

Abstract

Ensembl (https://www.ensembl.org) has produced high-quality genomic resources for vertebrates and model organisms for more than twenty years. During that time, our resources, services and tools have continually evolved in line with both the publicly available genome data and the downstream research and applications that utilise the Ensembl platform. In recent years we have witnessed a dramatic shift in the genomic landscape. There has been a large increase in the number of high-quality reference genomes through global biodiversity initiatives. In parallel, there have been major advances towards pangenome representations of higher species, where many alternative genome assemblies representing different breeds, cultivars, strains and haplotypes are now available. In order to support these efforts and accelerate downstream research, it is our goal at Ensembl to create high-quality annotations, tools and services for species across the tree of life. Here, we report our resources for popular reference genomes, the dramatic growth of our annotations (including haplotypes from the first human pangenome graphs), updates to the Ensembl Variant Effect Predictor (VEP), interactive protein structure predictions from AlphaFold DB, and the beta release of our new website.

Figure 1

AlphaFold structure prediction for the product of PPP2R2A. AlphaFold structures can be viewed through our new browser widget, via the ‘AlphaFold predicted model’ link in the left hand menu of any transcript page. Note that AlphaFold structures are currently limited to the primary coding transcript of each protein-coding gene, usually the one listed at the top of the transcript table.

Figure 2

Total annotations and species offered through Ensembl. This represents total annotations across all species where we have generated annotations through the Ensembl Annotation System (as of October 2022). Human has been given a separate category to reflect the large number of annotations generated as part of the HPRC.

Figure 3

Distribution of eukaryotic repeat libraries. RepeatModeler-derived libraries are now available on our FTP site for over 1100 species. These libraries are released as soon as the RepeatModeler analysis has completed. The ‘Other’ category includes molluscs, protists, arthropods and vertebrates not falling into the clades defined above.

Figure 4

Homepage for the new Ensembl website. The homepage acts as a gateway for interacting with our data via the species selector, genome browser and entity viewer apps. The new website will eventually bring all species across the current set of Ensembl websites under a single infrastructure.