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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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Patterns of DNA variation between the autosomes, the X chromosome and the Y chromosome in Bos taurus genome. / Czech, Bartosz; Guldbrandtsen, Bernt; Szyda, Joanna.

I: Scientific Reports, Bind 10, Nr. 1, 13641, 12.2020.

Publikation: Bidrag til tidsskrift/Konferencebidrag i tidsskrift /Bidrag til avisTidsskriftartikelForskningpeer review

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Czech, Bartosz ; Guldbrandtsen, Bernt ; Szyda, Joanna. / Patterns of DNA variation between the autosomes, the X chromosome and the Y chromosome in Bos taurus genome. I: Scientific Reports. 2020 ; Bind 10, Nr. 1.

Bibtex

@article{94f5b1cfa51d4d6cb31af9a8debd0e68,
title = "Patterns of DNA variation between the autosomes, the X chromosome and the Y chromosome in Bos taurus genome",
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{\textquoteright}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{\textquoteright}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.",
author = "Bartosz Czech and Bernt Guldbrandtsen and Joanna Szyda",
note = "Publisher Copyright: {\textcopyright} 2020, The Author(s). Copyright: Copyright 2020 Elsevier B.V., All rights reserved.",
year = "2020",
month = dec,
doi = "10.1038/s41598-020-70380-9",
language = "English",
volume = "10",
journal = "Scientific Reports",
issn = "2045-2322",
publisher = "Nature Publishing Group",
number = "1",

}

RIS

TY - JOUR

T1 - Patterns of DNA variation between the autosomes, the X chromosome and the Y chromosome in Bos taurus genome

AU - Czech, Bartosz

AU - Guldbrandtsen, Bernt

AU - Szyda, Joanna

N1 - Publisher Copyright: © 2020, The Author(s). Copyright: Copyright 2020 Elsevier B.V., All rights reserved.

PY - 2020/12

Y1 - 2020/12

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=85089374473&partnerID=8YFLogxK

U2 - 10.1038/s41598-020-70380-9

DO - 10.1038/s41598-020-70380-9

M3 - Journal article

C2 - 32788585

AN - SCOPUS:85089374473

VL - 10

JO - Scientific Reports

JF - Scientific Reports

SN - 2045-2322

IS - 1

M1 - 13641

ER -