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

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. Johnson, Richard P. Metz, Al Muatasim Al Zadjali, Charles C. Love, Dickson D. Varner, Daniel W. Bellott, William J. Murphy, Bhanu P. Chowdhary () and Terje Raudsepp ()
Additional contact information
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
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
Terje Raudsepp: Texas A&M University

Nature Communications, 2018, vol. 9, issue 1, 1-15

Abstract: 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.

Date: 2018
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DOI: 10.1038/s41467-018-05290-6

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