Telomere-to-telomere assemblies of cattle and sheep Y-chromosomes uncover divergent structure and gene content
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.
Authors
- Holly L. Neibergs (ORCID: https://orcid.org/0000-0001-8121-3072)
- Patricia Villamediana (ORCID: https://orcid.org/0009-0005-0726-6877)
- Morgan R Stegemiller (ORCID: https://orcid.org/0000-0001-9675-3047)
- Temitayo Olagunju (ORCID: https://orcid.org/0000-0002-1497-6173)
- Sergey Koren (ORCID: https://orcid.org/0000-0002-1472-8962)
- Kimberly M Davenport (ORCID: https://orcid.org/0000-0003-2796-9252)
- Amy L. Skibiel (ORCID: https://orcid.org/0000-0002-2729-0402)
- Timothy P. L. Smith (ORCID: https://orcid.org/0000-0003-1611-6828)
- Jacob W Thorne (ORCID: https://orcid.org/0000-0003-3553-7628)
- Brenda M. Murdoch (ORCID: https://orcid.org/0000-0001-8675-3473)
- Kristen L. Kuhn
- Gabrielle M. Becker (ORCID: https://orcid.org/0000-0002-1455-6443)
- Arang Rhie (ORCID: https://orcid.org/0000-0002-9809-8127)
- Katie A Shira (ORCID: https://orcid.org/0000-0002-2289-440X)
- Benjamin D. Rosen (ORCID: https://orcid.org/0000-0001-9395-8346)
- Noelle Cockett
- Christine G Elsik
- Tracy S. Hadfield
Institutions
- Utah State University (US)
- National Institutes of Health (US)
- Agricultural Research Service (US)
- University of Idaho (US)
- South Dakota State University (US)
- Angelo State University (US)
- National Human Genome Research Institute (US)
- Beltsville Agricultural Research Center (US)
- Roman L. Hruska U.S. Meat Animal Research Center (US)
- Washington State University (US)
- University of Missouri (US)
Publication Details
- Journal
- Nature Communications
- Published
- 2024-09-27
- DOI
- https://doi.org/10.1038/s41467-024-52384-5
- Citations
- 24
- Primary Topic
- Chromosomal and Genetic Variations
- Type
- article
- Field-Weighted Citation Impact
- 14.39
Funders
- U.S. Department of Agriculture
- National Institutes of Health
- National Institute of Food and Agriculture
- Agricultural Research Service
- National Human Genome Research Institute