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

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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.

Originalsprog	Engelsk
Tidsskrift	Nature Communications
Vol/bind	9
Udgave nummer	1
Antal sider	15
ISSN	2041-1723
DOI	https://doi.org/10.1038/s41467-018-05290-6
Status	Udgivet - 1 dec. 2018

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10.1038/s41467-018-05290-6Licens: CC BY

s41467-018-05290-6Forlagets udgivne version, 5,61 MBLicens: CC BY

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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). https://doi.org/10.1038/s41467-018-05290-6

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, bind 9, nr. 1. https://doi.org/10.1038/s41467-018-05290-6

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title = "Horse Y chromosome assembly displays unique evolutionary features and putative stallion fertility genes",

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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T1 - Horse Y chromosome assembly displays unique evolutionary features and putative stallion fertility genes

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

PY - 2018/12/1

Y1 - 2018/12/1

N2 - 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.

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.

U2 - 10.1038/s41467-018-05290-6

DO - 10.1038/s41467-018-05290-6

M3 - Journal article

C2 - 30054462

SN - 2041-1723

VL - 9

JO - Nature Communications

JF - Nature Communications

IS - 1

ER -

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

Abstract

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