Characterization of Copy Number Variation at the Equine Pseudoautosomal Region (PAR) Using Next Generation Sequencing

The pseudoautosomal region (PAR) is small region of homology between the X and Y sex chromosomes in mammals. The PAR is vital for segregation during meiosis and undergoes recombination. However, despite the plethora of genome sequencing projects, few species have an annotated PAR. The equine PAR was previously mapped on the X chromosome using FISH and BAC end sequences aligned to EquCab1.0, but there has been no attempt to leverage next generation sequencing data for finer resolution mapping. The current version of the equine genome (EquCab2.0) was constructed using Sanger sequencing of a female horse, and thus lacks Y chromosome sequence. We obtained Illumina sequencing reads from four females and four males of different breeds to align to the reference genome. The reference genome horse was included as one of the females to identify putative mis-assemblies on the X chromosome. Mapped read depth was used to estimate copy number across the genome. Calculated read depth values were averaged by gender at every base position across the X chromosome. As males only have one X chromosome, female-specific regions should display approximately half the copy number in males as compared to females. Thus, any regions displaying equal copy numbers for males and females are proposed to be pseudoautosomal in nature. Similarly, any deviations from a copy number of two in the genome horse are likely assembly errors. Copy number analysis is currently ongoing. Finer scale resolution of the equine PAR will help further our understanding of the evolution of sex chromosomes.