Towards a High-Standard Reference Genome of Horses with Whole Genome Physical Mapping and the Integration of Genome Sequences

A comprehensive approach to the construction of a genome map that integrates the sequence,  physical and genetic mapping data is essential whereas high-throughput physical mapping complements the whole process.  Using a single molecule genome mapping Irys technology, we constructed a high-quality reference genome physical map of the female Thoroughbred Twilight that was previously used for construction of the draft genome of domestic horse (Wade et al., 2009). The map had a 60x coverage of its estimated 2.7-Gb genome size, and spanned 2.5-Gb (over 90%) of the genome, with a minimal read size of 150 kb and an N50 of 1.3 Mb. The integrated physical and sequence map of Twilight has dramatically improved over the genome sequence, tenfold above the N50 of 112 kb in EquCab2, helped close 5,131 gaps between the larger contigs, and identified 142 variants, compared to EquCab2, that are up to 60 kb additional or missing DNA. In a close-up view of the equine MHC region of 6.5 Mb on Chromosome 20 it was covered up to 97% and 95% (128/135) known gaps in the sequence draft were filled in this region by the physical map. Comparison of this assembly to a horse genome physical map that we generated earlier (ISAG2014, Xian, China) revealed the regions of conservation and divergence between the two animals, including 502 CNVs with an average size of 17 kb.  The availability of a high-standard reference genome of horses should lay an improved foundation for horse genetic research and breeding, and open a new avenue for advanced biological studies in equine sciences.