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

Author

Listed:
  • 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)

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.

Suggested Citation

  • 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 & Kati, 2024. "Telomere-to-telomere assemblies of cattle and sheep Y-chromosomes uncover divergent structure and gene content," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-52384-5
    DOI: 10.1038/s41467-024-52384-5
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    1. Arang Rhie & Sergey Nurk & Monika Cechova & Savannah J. Hoyt & Dylan J. Taylor & Nicolas Altemose & Paul W. Hook & Sergey Koren & Mikko Rautiainen & Ivan A. Alexandrov & Jamie Allen & Mobin Asri & And, 2023. "The complete sequence of a human Y chromosome," Nature, Nature, vol. 621(7978), pages 344-354, September.
    2. David R. Bentley & Shankar Balasubramanian & Harold P. Swerdlow & Geoffrey P. Smith & John Milton & Clive G. Brown & Kevin P. Hall & Dirk J. Evers & Colin L. Barnes & Helen R. Bignell & Jonathan M. Bo, 2008. "Accurate whole human genome sequencing using reversible terminator chemistry," Nature, Nature, vol. 456(7218), pages 53-59, November.
    3. Kateryna D. Makova & Brandon D. Pickett & Robert S. Harris & Gabrielle A. Hartley & Monika Cechova & Karol Pal & Sergey Nurk & DongAhn Yoo & Qiuhui Li & Prajna Hebbar & Barbara C. McGrath & Francesca , 2024. "The complete sequence and comparative analysis of ape sex chromosomes," Nature, Nature, vol. 630(8016), pages 401-411, June.
    4. Mark T. Ross & Darren V. Grafham & Alison J. Coffey & Steven Scherer & Kirsten McLay & Donna Muzny & Matthias Platzer & Gareth R. Howell & Christine Burrows & Christine P. Bird & Adam Frankish & Franc, 2005. "The DNA sequence of the human X chromosome," Nature, Nature, vol. 434(7031), pages 325-337, March.
    5. Zhe-Xi Luo & Chong-Xi Yuan & Qing-Jin Meng & Qiang Ji, 2011. "A Jurassic eutherian mammal and divergence of marsupials and placentals," Nature, Nature, vol. 476(7361), pages 442-445, August.
    6. Karen H. Miga & Sergey Koren & Arang Rhie & Mitchell R. Vollger & Ariel Gershman & Andrey Bzikadze & Shelise Brooks & Edmund Howe & David Porubsky & Glennis A. Logsdon & Valerie A. Schneider & Tamara , 2020. "Telomere-to-telomere assembly of a complete human X chromosome," Nature, Nature, vol. 585(7823), pages 79-84, September.
    7. Jennifer F. Hughes & Helen Skaletsky & Laura G. Brown & Tatyana Pyntikova & Tina Graves & Robert S. Fulton & Shannon Dugan & Yan Ding & Christian J. Buhay & Colin Kremitzki & Qiaoyan Wang & Hua Shen &, 2012. "Strict evolutionary conservation followed rapid gene loss on human and rhesus Y chromosomes," Nature, Nature, vol. 483(7387), pages 82-86, March.
    8. Diego Cortez & Ray Marin & Deborah Toledo-Flores & Laure Froidevaux & Angélica Liechti & Paul D. Waters & Frank Grützner & Henrik Kaessmann, 2014. "Origins and functional evolution of Y chromosomes across mammals," Nature, Nature, vol. 508(7497), pages 488-493, April.
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