EquCab3: An Improved Genomic Reference for the Domestic Horse

An updated version of the reference genome for the domestic horse, EquCab3, is nearing completion. The previous version, EquCab2, was completed in 2007 and published in 2009 (Wade et al., Science 2009). The 2007 version was derived entirely from 30 million Sanger reads comprising ~6.8X genomic coverage. It has since served well as the foundation for nearly all genetic and genomic studies for most Equid species. Advances in Next Generation Sequencing technology, including new PCR free library preps with less bias against gc-rich sequences, have made it possible for us to improve contiguity in excess of 10 fold measured by both contig and scaffold N50 values. Additionally, we present evidence of improved contiguity near the 5’ end of annotated genes which should help significantly as we endeavor to understand the role of genetics in gene regulatory processes. A pre-release version of EquCab3 is currently being evaluated by the Equine research community, and will be ready for final release to annotation groups in early 2017.