Abstract
The new ARS-UCD1.2 assembly of the bovine genome has considerable improvements over the previous assembly and thus 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, variant densities, annotations, lengths (only for InDels), nucleotide divergence, and Tajima’s D statistics between chromosomes were considered. 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 identification. 23,655,295 SNPs and 3,758,781 InDels were detected. In contrast to autosomes, both sex chromosomes had negative values of Tajima’s D and lower nucleotide divergence. That implies a correlation between nucleotide diversity and recombination rate, which is obviously reduced for sex chromosomes. Moreover, the 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.
Highlights
DNA variation refers to differences in DNA sequence among individuals
A high percent of mapped reads, a high percent of properly mapped paired reads, and the fact that the most of individual genomes were sequenced with a genome average coverage exceeding twenty, demonstrated high quality of our data allowing for reliable inferences
InDels in transcription regions are highly deleterious to gene function as they can completely alter protein amino acid sequence by changing the open reading frame
Summary
DNA variation refers to differences in DNA sequence among individuals. Decreasing costs and reducing the time of whole-genome sequencing using the Next-Generation Sequencing (NGS) technology brings the opportunity to sequence many samples. We used the new ARS-UCD 1.0.25 assembly that is the latest and the most accurate (less gaps) version of the cattle reference genome[1]. This assembly, like the UMD3.12, does not contain the bovine Y chromosome (BTY), so most analyzes ignored the Y chromosome. The bovine X chromosome (BTX) contains many more genes and its length is similar to the BTA2. Since recombination that generates new combinations of alleles is characteristic to autosomes, on sex chromosomes, this phenomenon is reduced in males to only small homologous regions shared between BTX and -Y, called the pseudoautosomal regions (PARs). The focus of our study was on the comparison of patterns of genetic variation between autosomes, the X chromosome, and the Y chromosome in the context of the bovine genome
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