Ensembl 2024

Abstract

Ensembl (https://www.ensembl.org) is a freely available genomic resource that has produced high-quality annotations, tools, and services for vertebrates and model organisms for more than two decades. In recent years, there has been a dramatic shift in the genomic landscape, with a large increase in the number and phylogenetic breadth of high-quality reference genomes, alongside major advances in the pan-genome representations of higher species. In order to support these efforts and accelerate downstream research, Ensembl continues to focus on scaling for the rapid annotation of new genome assemblies, developing new methods for comparative analysis, and expanding the depth and quality of our genome annotations. This year we have continued our expansion to support global biodiversity research, doubling the number of annotated genomes we support on our Rapid Release site to over 1700, driven by our close collaboration with biodiversity projects such as Darwin Tree of Life. We have also strengthened support for key agricultural species, including the first regulatory builds for farmed animals, and have updated key tools and resources that support the global scientific community, notably the Ensembl Variant Effect Predictor. Ensembl data, software, and tools are freely available.

Graphical Abstract

Figure 1.

Annotations available on Ensembl Rapid release site. (A) Taxonomic breakdown and numbers of all annotations (‘distant vertebrates’ includes sharks and cartilaginous fish). (B) Increasing number of annotations available via Rapid Release since its inception in June 2020. The total number of genomes available each month (green bars) and the total number of unique species (blue bars).

Figure 2.

Ensembl provides comprehensive regulatory annotation for human and mouse using data from the ENCODE & BLUEPRINT projects. From Ensembl release 110, regulatory annotation of promoters and open chromatin has been extended to farmed animals. Future work will relabel some of the new open chromatin regions as enhancers based on overlap with relevant histone ChIP-seq peaks.

Figure 3.

Novel rendering of variants in new Ensembl website. rs756076618, a short variant from dbSNP that lies close to a splice site in the MANE Select transcript for FGFR2, has been selected as the focus object. Variants are coloured according to group, and the browser can optionally be configured to display identifiers, alleles and the extent of the reference sequence affected.