Telomere-to-telomere assemblies of cattle and sheep Y-chromosomes uncover divergent structure and gene content

Temitayo A. Olagunju, Benjamin D. Rosen, Holly L. Neibergs, Gabrielle M. Becker, Kimberly M. Davenport, Christine G. Elsik, Tracy S. Hadfield, Sergey Koren, Kristen L. Kuhn, Arang Rhie, Katie A. Shira, Amy L. Skibiel, Morgan R. Stegemiller, Jacob W. Thorne, Patricia Villamediana, Noelle E. Cockett, Brenda M. Murdoch () and Timothy P. L. Smith ()
Additional contact information
Temitayo A. Olagunju: University of Idaho
Benjamin D. Rosen: ARS, USDA
Holly L. Neibergs: Washington State University
Gabrielle M. Becker: University of Idaho
Kimberly M. Davenport: Washington State University
Christine G. Elsik: University of Missouri
Tracy S. Hadfield: Utah State University
Sergey Koren: National Human Genome Research Institute, National Institutes of Health
Kristen L. Kuhn: U.S. Meat Animal Research Center (USMARC), ARS, USDA
Arang Rhie: National Human Genome Research Institute, National Institutes of Health
Katie A. Shira: University of Idaho
Amy L. Skibiel: University of Idaho
Morgan R. Stegemiller: University of Idaho
Jacob W. Thorne: Texas A&M AgriLife Extension
Patricia Villamediana: South Dakota State University
Noelle E. Cockett: Utah State University
Brenda M. Murdoch: University of Idaho
Timothy P. L. Smith: U.S. Meat Animal Research Center (USMARC), ARS, USDA

Nature Communications, 2024, vol. 15, issue 1, 1-12

Abstract: Abstract Reference genomes of cattle and sheep have lacked contiguous assemblies of the sex-determining Y chromosome. Here, we assemble complete and gapless telomere to telomere (T2T) Y chromosomes for these species. We find that the pseudo-autosomal regions are similar in length, but the total chromosome size is substantially different, with the cattle Y more than twice the length of the sheep Y. The length disparity is accounted for by expanded ampliconic region in cattle. The genic amplification in cattle contrasts with pseudogenization in sheep suggesting opposite evolutionary mechanisms since their divergence 19MYA. The centromeres also differ dramatically despite the close relationship between these species at the overall genome sequence level. These Y chromosomes have been added to the current reference assemblies in GenBank opening new opportunities for the study of evolution and variation while supporting efforts to improve sustainability in these important livestock species that generally use sire-driven genetic improvement strategies.

Date: 2024
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DOI: 10.1038/s41467-024-52384-5

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