RT Journal Article
SR Electronic
T1 Large palindromes on the primate X Chromosome are preserved by natural selection
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2020.12.29.424738
DO 10.1101/2020.12.29.424738
A1 Emily K. Jackson
A1 Daniel W. Bellott
A1 Ting-Jan Cho
A1 Helen Skaletsky
A1 Jennifer F. Hughes
A1 Tatyana Pyntikova
A1 David C. Page
YR 2020
UL http://biorxiv.org/content/early/2020/12/29/2020.12.29.424738.abstract
AB Mammalian sex chromosomes carry large palindromes that harbor protein-coding gene families with testis-biased expression. However, there are few known examples of sex-chromosome palindromes conserved between species. We identified 26 palindromes on the human X Chromosome, constituting more than 2% of its sequence, and characterized orthologous palindromes in the chimpanzee and the rhesus macaque using a clone-based sequencing approach that incorporates full-length nanopore reads. Many of these palindromes are missing or misassembled in the current reference assemblies of these species’ genomes. We find that 12 human X palindromes have been conserved for at least 25 million years, with orthologs in both chimpanzee and rhesus macaque. Insertions and deletions between species are significantly depleted within the X palindromes’ protein-coding genes compared to their non-coding sequence, demonstrating that natural selection has preserved these gene families. Unexpectedly, the spacers that separate the left and right arms of palindromes are a site of localized structural instability, with 7 of 12 conserved palindromes showing no spacer orthology between human and rhesus macaque. Analysis of the 1000 Genomes Project dataset revealed that human X-palindrome spacers are enriched for deletions relative to arms and flanking sequence, including a common spacer deletion that affects 13% of human X Chromosomes. This work reveals an abundance of conserved palindromes on primate X Chromosomes, and suggests that protein-coding gene families in palindromes (most of which remain poorly characterized) promote X-palindrome survival in the face of ongoing structural instability.Competing Interest StatementThe authors have declared no competing interest.