Functionally Annotated Equine Pangenome with Infrastructure for an Accessible, Integrative, Community Genomics Resource

Abstract: Inexpensive and accurate high throughput sequencing has made it possible to begin to understand the genetic basis of health and performance in animals. In agricultural applications, these data have exposed the limitations of a single reference genome for a species. It is now feasible to create many reference genomes of individual breeds, providing for the impact of breed-specific genetic, epigenetic, and structural differences to be elucidated. A pan-genome allows for the integration of multiple reference genomes with their associated annotation and variant data to facilitate discovery. Our long-term goal is to provide tools and readily accessible data to expedite efforts to connect genome to phenome. In this proposal we will build upon prior community efforts to address our goal by: 1) creating a pan-genome from accurate, haplotype-resolved genome assemblies of 13 target breeds and 3 related Equids, 2) annotate the pan-genome using tissue-specific transcriptomic and epigenetic data, and 3) developing and making available an integrative genomics portal. As an outcome of this work, in line with FAIR principles, we will have tools necessary for anyone to quickly and easily access community-generated genomics data without bioinformatics training. The methodology developed for analyses and data access can be applied across species. Our team iswell-positioned to do this work, which fits into the blueprint area of "Developing Advanced Genomic Tools, Technologies, and Resources for Agricultural Animals," given our prior experience in haplotype-resolved genome assembly and bioinformatic methodology, a significant amount of data on hand, and the support of a highly collaborative community.