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.

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Published in Nature Communications, v. 9, article no. 2945, p. 1-15.

© The Author(s) 2018

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This work was supported by USDA (grant 2012-67015-19632, BPC, TR, JEJ), LINK Endowment Equine Foundation (BPC, TR), Danish National Research Foundation (grant DNRF94, LO, MS), Initiative d′Excellence Chaires d′attractivité, Université de Toulouse (OURASI, LO), the European Research Council (grant agreement ERC-CoG-2015-681605, LO, MS).

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Sequences and metadata generated in this work are publicly available. BioProject Accession PRJNA420505 includes information about project, samples, and SRA accessions including SRR636826-SRR636831 for RNAseq reads of 6 samples from 2 horses, 2 donkeys, 2 mules) and SRR6361136-SRR6361138 (for 54 single-end reads and mate-pair reads for tiling path BACs, and Illumina paired-end reads of individually barcoded multi-copy BACs. The eMSYv3.1 assembly has been deposited in GenBank under accession number MH341179. In the v3.1 accession, two vector sequences (18,381-bp in position 2,505,950 and 1396-bp in position 8,066,811) have been trimmed from assembly with respect to v3.0. The GTF file for v3.0 available as Supplementary Data 2 with information on how to modify v3.1 assembly to match the v3.0 GTF annotations used in our analysis. GenBank accessions to BAC end sequences, MSY STS sequences and Sanger sequences of Parascaris samples can be found in Supplementary Data 4 and 7.

Supplementary Information accompanies this paper at https://doi.org/10.1038/s41467-018-05290-6.

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