Ensembl 2025

Abstract

Ensembl (www.ensembl.org) is an open platform integrating publicly available genomics data across the tree of life with a focus on eukaryotic species related to human health, agriculture and biodiversity. This year has seen a continued expansion in the number of species represented, with >4800 eukaryotic and >31 300 prokaryotic genomes available. The new Ensembl site, currently in beta, has continued to develop, currently holding >2700 eukaryotic genome assemblies. The new site provides genome, gene, transcript, homology and variation views, and will replace the current Rapid Release site; this represents a key step towards provision of a single integrated Ensembl site. Additional activities have included developing improved regulatory annotation for human, mouse and agricultural species, and expanding the Ensembl Variant Effect Predictor tool. To learn more about Ensembl, help and documentation are available along with an extensive training program that can be accessed via our training pages.

Graphical Abstract

Figure 1.. Distribution of eukaryotic species with genomes available across all Ensembl sites. The distribution of eukaryotic species with available genomes from all Ensembl sites is represented based on NCBI taxonomy, highlighting the hierarchical relationships among taxa and their lineages. The tree was estimated through the NCBI interface of ETE3 (43) and annotated using iTOL (44). The coloured circle represents the high-level taxonomic division to which the species in the corresponding region of the tree

belong.

Figure 2.

Ensembl location view of the human gene HK1 showing MANE Select, MANE Plus Clinical and GENCODE Primary transcripts. Screenshot of the HK1 gene on human GRCh38 assembly chromosome 10 from Ensembl release 112 (https://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000156515). The GENCODE Primary set will reduce the number of transcripts in the default view to 3 (MANE Select, MANE Plus Clinical and GENCODE Primary) from the complete set of 30 (screenshot truncated) from the GENCODE Comprehensive set. Greyed out transcripts are those not contained within the GENCODE basic set, which has 12 transcripts for this gene.

Figure 3.

Screenshot of the Variation Entity Viewer overview of transcript consequences tab. The focus variant (rs580358533) is a single nucleotide variant in exon 10 of the BRCA2 gene and the predicted molecular consequence is stop_gained, relative to the MANE select transcript, as shown in the central panel. Allele frequency data are available from the Allele frequency tab, which is the fourth tab from the left on the top. The variant can be viewed at https://beta.ensembl.org/entity-viewer/grch38/variant:13:32337185:rs80358533?allele=0&view=transcript-consequences.