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

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  • Bartosz Czech, Wroclaw University of Environmental and Life Sciences
  • ,
  • Bernt Guldbrandtsen, University of Bonn
  • ,
  • Joanna Szyda, Wroclaw University of Environmental and Life Sciences, Institute of Animal Breeding

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.

OriginalsprogEngelsk
Artikelnummer13641
TidsskriftScientific Reports
Vol/bind10
Nummer1
ISSN2045-2322
DOI
StatusUdgivet - dec. 2020

Bibliografisk note

Publisher Copyright:
© 2020, The Author(s).

Copyright:
Copyright 2020 Elsevier B.V., All rights reserved.

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