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; Terje Raudsepp

doi:10.1038/s41467-018-05290-6

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, Terje Raudsepp

Research output: Contribution to journal › Article › Academic › peer-review

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.

Original language	English
Article number	2945
Journal	Nature Communications
Volume	9
Issue number	1
DOIs	https://doi.org/10.1038/s41467-018-05290-6
Publication status	Published - 27 Jul 2018

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Janečka, J. E., Davis, B. W., Ghosh, S., Paria, N., Das, P. J., Orlando, L., Schubert, M., Nielsen, M. K., Stout, T. A. E., Brashear, W., Li, G., Johnson, C. D., Metz, R. P., Zadjali, A. M. A., Love, C. C., Varner, D. D., Bellott, D. W., Murphy, W. J., Chowdhary, B. P., & Raudsepp, T. (2018). Horse Y chromosome assembly displays unique evolutionary features and putative stallion fertility genes. Nature Communications, 9(1), Article 2945. https://doi.org/10.1038/s41467-018-05290-6

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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.",

author = "Jane{\v c}ka, {Jan E} and Davis, {Brian W} and Sharmila Ghosh and Nandina Paria and Das, {Pranab J} and Ludovic Orlando and Mikkel Schubert and Nielsen, {Martin K} and Stout, {Tom A E} and Wesley Brashear and Gang Li and Johnson, {Charles D} and Metz, {Richard P} and Zadjali, {Al Muatasim Al} and Love, {Charles C} and Varner, {Dickson D} and Bellott, {Daniel W} and Murphy, {William J} and Chowdhary, {Bhanu P} and Terje Raudsepp",

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Janečka, JE, Davis, BW, Ghosh, S, Paria, N, Das, PJ, Orlando, L, Schubert, M, Nielsen, MK, Stout, TAE, Brashear, W, Li, G, Johnson, CD, Metz, RP, Zadjali, AMA, Love, CC, Varner, DD, Bellott, DW, Murphy, WJ, Chowdhary, BP & Raudsepp, T 2018, 'Horse Y chromosome assembly displays unique evolutionary features and putative stallion fertility genes', Nature Communications, vol. 9, no. 1, 2945. https://doi.org/10.1038/s41467-018-05290-6

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AU - Janečka, Jan E

AU - Davis, Brian W

AU - Ghosh, Sharmila

AU - Paria, Nandina

AU - Das, Pranab J

AU - Orlando, Ludovic

AU - Schubert, Mikkel

AU - Nielsen, Martin K

AU - Stout, Tom A E

AU - Brashear, Wesley

AU - Li, Gang

AU - Johnson, Charles D

AU - Metz, Richard P

AU - Zadjali, Al Muatasim Al

AU - Love, Charles C

AU - Varner, Dickson D

AU - Bellott, Daniel W

AU - Murphy, William J

AU - Chowdhary, Bhanu P

AU - Raudsepp, Terje

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AB - 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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ER -

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

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