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Horse Y chromosome assembly displays unique evolutionary features and putative stallion fertility genes

Author

Listed:
  • Jan E. Janečka

    (Duquesne University)

  • Brian W. Davis

    (Texas A&M University)

  • Sharmila Ghosh

    (Texas A&M University)

  • Nandina Paria

    (Texas Scottish Rite Hospital for Children)

  • Pranab J. Das

    (ICAR-National Research Centre on Pig)

  • Ludovic Orlando

    (Natural History Museum of Denmark
    Université de Toulouse, Université Paul Sabatier)

  • Mikkel Schubert

    (Natural History Museum of Denmark)

  • Martin K. Nielsen

    (University of Kentucky)

  • Tom A. E. Stout

    (Utrecht University)

  • Wesley Brashear

    (Texas A&M University)

  • Gang Li

    (Texas A&M University)

  • Charles D. Johnson

    (Texas A&M AgriLife Research)

  • Richard P. Metz

    (Texas A&M AgriLife Research)

  • Al Muatasim Al Zadjali

    (Duquesne University)

  • Charles C. Love

    (Texas A&M University)

  • Dickson D. Varner

    (Texas A&M University)

  • Daniel W. Bellott

    (Whitehead Institute in Cambridge)

  • William J. Murphy

    (Texas A&M University)

  • Bhanu P. Chowdhary

    (Texas A&M University
    United Arab Emirates University)

  • Terje Raudsepp

    (Texas A&M University)

Abstract

Dynamic evolutionary processes and complex structure make the Y chromosome among the most diverse and least understood regions in mammalian genomes. Here, we present an annotated assembly of the male specific region of the horse Y chromosome (eMSY), representing the first comprehensive Y assembly in odd-toed ungulates. The eMSY comprises single-copy, equine specific multi-copy, PAR transposed, and novel ampliconic sequence classes. The eMSY gene density approaches that of autosomes with the highest number of retained X–Y gametologs recorded in eutherians, in addition to novel Y-born and transposed genes. Horse, donkey and mule testis RNAseq reveals several candidate genes for stallion fertility. A novel testis-expressed XY ampliconic sequence class, ETSTY7, is shared with the parasite Parascaris genome, providing evidence for eukaryotic horizontal transfer and inter-chromosomal mobility. Our study highlights the dynamic nature of the Y and provides a reference sequence for improved understanding of equine male development and fertility.

Suggested Citation

  • Jan E. Janečka & Brian W. Davis & Sharmila Ghosh & Nandina Paria & Pranab J. Das & Ludovic Orlando & Mikkel Schubert & Martin K. Nielsen & Tom A. E. Stout & Wesley Brashear & Gang Li & Charles D. John, 2018. "Horse Y chromosome assembly displays unique evolutionary features and putative stallion fertility genes," Nature Communications, Nature, vol. 9(1), pages 1-15, December.
    • Handle: RePEc:nat:natcom:v:9:y:2018:i:1:d:10.1038_s41467-018-05290-6
    DOI: 10.1038/s41467-018-05290-6
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