Gene function & annotation

Ensembl in a new era: providing annotation resources for the many breeds and populations of domestic animals

---

Abstract

Ensembl (www.ensembl.org) is an open platform which enables visualisation and discovery of domestic animal genomes by integrating publicly available data for an extensive range of species, breeds and populations. It generates genomic annotations, functional predictions and comparative resources and aggregates public data to display genetic variants and phenotype associations. Ensembl has recently launched a new unified infrastructure and web interface (https://beta.ensembl.org), with a state of the art genome browser, that is designed to provide new data updates every two to three weeks. At the same time domestic animal genomics is rapidly shifting from a single incomplete reference genome per species towards telomere-to-telomere (T2T) genomes and multiple high-quality assemblies per breed/population, alongside a rapid growth in functional genomics datasets (long-read transcriptomics, epigenomes). This represents a challenge but also a unique opportunity and will shape how we provide resources for domestic animals in Ensembl both now and in the future. Taking chicken as example, Ensembl has recently provided genome regulatory annotation (https://regulation.ensembl.org), for ten species, including chicken on the GRCg7b assembly. Our chicken regulatory annotation was produced by processing primary data generated for the US-led Functional Annotation in Animal Genomes (FAANG) project for chicken, and the H2020 EuroFAANG project GENE-SWitCH funded by the European Commission. Our annotation for chicken provides information for the location of promoters, enhancers, and CTCF-binding sites, allowing researchers to explore regulatory activity across the chicken genome. For chicken we also provide layers of additional annotation information including CADD and other variant prioritization scores, a multi-way progressive cactus alignment for 10 poultry species, and we are working on providing structural variants views. We currently also provide these resources for pig and five farmed fish species and will extend them to include cattle and sheep. These resources, particularly our regulatory annotations, rely on very high-quality data and metadata which is brokered through the data portal for the Functional Annotation of Animal Genomes (FAANG) project (https://data.faang.org/home) into the public archives. We have recently significantly improved the submission and validation tools and updated the FAANG Data Portal infrastructure to provide the domestic animal genomics community with a more efficient route for data submission. Together these resources underpin domestic animal genomics research globally. Key considerations now include integrating the T2T genomes as the anchor for these resources, adding value by lifting existing annotations across to the breed-specific assemblies, and identifying datasets to train machine learning models to predict genomic features and variant effects. The transition to the new Ensembl infrastructure, and timing of WCGALP, represents the ideal opportunity to present a vision for these resources and ask for community feedback into how we can best meet the future needs of all stakeholders.

Keywords: 2026

How to Cite:

Martin, F., Allen, J., Archibald, A., Brooks, L., Branco-Lins, P., Cezard, T., Cheema, J., Eory, L., Haggerty, L., Hall, H., Harrison, P., Hunt, S., Ilsley, G., Kaur-Bhurji, S., Loveland, J., Merino, G., Perez-Silva, J., Sipos, B., Smith, J., Sokolov, A., Tricomi, F., Urbina-Gómez, D., Walsh, T., Prendergast, J. & Clark, E., (2026) “Ensembl in a new era: providing annotation resources for the many breeds and populations of domestic animals”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2286915. doi: https://doi.org/10.31274/wcgalp.24163

Rights: 1