Ensembl in a new era - deep genome annotation of domesticated animal species and breeds

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The Ensembl genome browser is a widely used web-based interface that makes deeply annotated reference genomes for domesticated animals available in a unified way to researchers. An explosion in the number of genomes produced for domesticated animals is expected in the coming three years. In this proposal we describe how we will ensure that the Ensembl genome browser can keep pace to provide deep annotation of these genomes.

Populations of domesticated animals are diverse, including many different breeds and populations within each species. Advances in sequencing technologies means that the recent rise in the number of assembled genomes for domesticated animal species is expected to continue and accelerate. However:

- Current Ensembl resources are primarily focused around individual reference genomes for a single or a small number of representatives per species.
- New ways of storing, comparing, annotating, visualising and making available the diversity of genomes for each domesticated animal species are urgently required.
- Support for efforts to annotate this wealth of genome sequence data in a timely manner is critical to realising the potential impact of these data.

The overarching aim of this proposal is to establish and maintain deeply annotated genomes for domesticated animal species in the Ensembl genome browser. To achieve this aim we will:

- Analyse and annotate domesticated animal genomes as they become available, including alternate assemblies, exploiting the growing volumes of functional data.
- Run comparative genomics analyses both between species and within species.
- Acquire data from re-sequencing projects to characterise genetic variation within species and annotate variants by genomic region.

To ensure that the research community can make the most efficient use of the resource we will provide training and ensure we regularly adjust our priorities based on user feedback.