Horse Y chromosome assembly displays unique evolutionary features and putative stallion fertility genes. Academic Article uri icon


  • 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.

published proceedings

  • Nat Commun

altmetric score

  • 14.5

author list (cited authors)

  • Janeka, J. E., Davis, B. W., Ghosh, S., Paria, N., Das, P. J., Orlando, L., ... Raudsepp, T.

citation count

  • 46

complete list of authors

  • Janečka, Jan E||Davis, Brian W||Ghosh, Sharmila||Paria, Nandina||Das, Pranab J||Orlando, Ludovic||Schubert, Mikkel||Nielsen, Martin K||Stout, Tom AE||Brashear, Wesley||Li, Gang||Johnson, Charles D||Metz, Richard P||Zadjali, Al Muatasim Al||Love, Charles C||Varner, Dickson D||Bellott, Daniel W||Murphy, William J||Chowdhary, Bhanu P||Raudsepp, Terje

publication date

  • January 2018