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

• Published in: Nature communications Vol. 9; no. 1; pp. 2945 - 15
• Main Authors: Janečka, Jan E., Davis, Brian W., Ghosh, Sharmila, Paria, Nandina, Das, Pranab J., Orlando, Ludovic, Schubert, Mikkel, Nielsen, Martin K., Stout, Tom A. E., 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
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 27.07.2018; Nature Publishing Group; Nature Portfolio
• Subjects: 13; 14; 14/32; 45; 45/22; 45/23; 45/77; 45/88; 45/90; 45/91; 631/181/735; 631/208/212/748; Animals; Ascaridoidea - genetics; Assembly; Biological evolution; Chromosomes; Equidae - genetics; Evolution, Molecular; Fertility; Fertility - genetics; Gene Dosage - genetics; Gene Transfer, Horizontal; Genes; Genomes; Horizontal transfer; Horses - genetics; Humanities and Social Sciences; Hybridization, Genetic; Male; multidisciplinary; Nucleotide sequence; Phylogeny; Science; Science (multidisciplinary); Testis - metabolism; Ungulates; X Chromosome - genetics; Y Chromosome - genetics; Y Chromosomes
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-018-05290-6

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. The rapidly evolving Y chromosome accumulates male-benefit genes but is often poorly characterized in many mammals. Here, the authors assemble the male specific region of the horse Y chromosome and investigate its evolution and function.