176 Functional Annotation of the Equine Genome: from Sample Collection to Fair Data

Abstract The equine Functional Annotation of Animal Genomes (FAANG) project has worked over the past 6 years to generate publicly available transcriptomic and epigenetic data. From biobanks of carefully phenotyped and preserved samples of four Thoroughbred horses (2 mares and 2 stallions), annotation assays are complete on a set of “prioritized” tissues. Study of four histone modification marks revealed hundreds of thousands of previously unidentified regulatory regions across the genome, providing for information on individual tissues and between sexes. ATAC-seq was used to identify open chromatin on nine tissues of each sex elucidating over 300,000 open chromatin regions. Open chromatin regions, many tissue-specific, were enriched in transcription start and stop sites, exons, and promoters of genes. In addition to regulatory regions, long-read transcriptome sequencing has helped to elucidate a wealth of new isoforms within and among tissues that have greatly improved the annotation of the coding genome. The horse also represents a unique model to study centromere function. ChIP-seq studies identified repressive histone marks and a lack of transcription near the satellite-less centromere of chromosome 11, the position of which varies among individuals but not among tissues within an individual. Not only have key genomic features been identified, but the team has developed an Equine Genome Portal. This portal allows anyone to access raw and derived data and utilize data without having to download the entire dataset or recreate analyses. This community effort continues to supplement the current genome annotation while making all data available to enrich the potential of equine and evolutionary research.