Journal
GENOME BIOLOGY AND EVOLUTION
Volume 12, Issue 6, Pages 842-859Publisher
OXFORD UNIV PRESS
DOI: 10.1093/gbe/evaa088
Keywords
great apes; Y chromosome; ampliconic genes; gene copy number; gene expression; bonobo; orangutan
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Funding
- National Institute of General Medical Sciences of the National Institutes of Health (NIH) [R01GM130691]
- Clinical and Translational Sciences Institute at Pennsylvania State University
- Institute of Computational and Data Science at Pennsylvania State University
- Eberly College of Sciences-at Pennsylvania State University
- Pennsylvania Department of Health
- PSU-NIH
- National Science Foundation (NSF) [DBI-1356529, IIS-1453527, IIS1421908, CCF-1439057]
- NIH [R35GM128590]
- Alfred P. Sloan Foundation
- NSF [DEB-1753489, DEB-1949268, BCS-2001063]
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Multicopy ampliconic gene families on the Y chromosome play an important role in spermatogenesis. Thus, studying their genetic variation in endangered great ape species is critical. We estimated the sizes (copy number) of nine Y ampliconic gene families in population samples of chimpanzee, bonobo, and orangutan with droplet digital polymerase chain reaction, combined these estimates with published data for human and gorilla, and produced genome-wide testis gene expression data for great apes. Analyzing this comprehensive data set within an evolutionary framework, we, first, found high inter- and intraspecific variation in gene family size, with larger families exhibiting higher variation as compared with smaller families, a pattern consistent with random genetic drift. Second, for four gene families, we observed significant interspecific size differences, sometimes even between sister species-chimpanzee and bonobo. Third, despite substantial variation in copy number, Y ampliconic gene families' expression levels did not differ significantly among species, suggesting dosage regulation. Fourth, for three gene families, size was positively correlated with gene expression levels across species, suggesting that, given sufficient evolutionary time, copy number influences gene expression. Our results indicate high variability in size but conservation in gene expression levels in Y ampliconic gene families, significantly advancing our understanding of Y-chromosome evolution in great apes.
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