Patterns of DNA variation between the autosomes, the X chromosome and the Y chromosome in Bos taurus genome

The new ARS-UCD1.2 assembly of the bovine genome has considerable improvements. That might be assumed that a more accurate identification of patterns of genetic variation can be achieved with it. We explored differences in genetic variation between autosomes, the X chromosome, and the Y chromosome. In particular, densities of variants, annotation, lengths (only for InDels), nucleotide divergence, and Tajimas D statistic between chromosomes. Whole-genome DNA sequences of 217 individuals representing different cattle breeds were examined. The analysis included the alignment to the new reference genome and variant calling. 23,655,295 SNPs and 3,758,781 InDels were detected. In contrast to autosomes, both sex chromosomes had negative values of Tajimas D and lower nucleotide divergence. That implies a correlation between nucleotide diversity and recombination rate, which is obviously reduced for sex chromosomes. Moreover, accumulation of nonsynonymous mutations on the Y chromosome could be associated with loss of recombination. Also, the relatively lower effective population size for sex chromosomes leads to a lower expected density of variants.