Protein-Coding Gene Sequences Quantify Progress Toward the New Equine Reference Genome Assembly

The current version of the equine reference genome (EquCab2) was assembled entirely from Sanger sequence reads and published in 2009. Due to limited sequence read coverage and technological issues with Sanger data, some functional genes that are highly conserved in other mammals are not present in EquCab2. In our continuing effort to improve the equine reference genome’s utility, we have applied new sequence data from the reference horse (Twilight) to map and annotate protein-coding genes missing from EquCab2. The new genomic assembly, along with RNA-Seq data, incorporates many of these genes into chromosomes. In addition, we report major improvements to the N50 and L50 statistics, as well as a significantly reduced number of ambiguous nucleotides. Finally, we have identified a number of small, unassembled contigs in our assembly as either contaminant sequences or structural variants found in Twilight. These improvements to the equine reference genome will be valuable for subsequent genomic and transcriptomic studies of the horse.