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An 8.22 Mb Assembly and Annotation of the Alpaca (Vicugna pacos) Y Chromosome

The unique evolutionary dynamics and complex structure make the Y chromosome the most diverse and least understood region in the mammalian genome, despite its undisputable role in sex determination, development, and male fertility. Here we present the first contig-level annotated draft assembly for...

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Autores principales: Jevit, Matthew J., Davis, Brian W., Castaneda, Caitlin, Hillhouse, Andrew, Juras, Rytis, Trifonov, Vladimir A., Tibary, Ahmed, Pereira, Jorge C., Ferguson-Smith, Malcolm A., Raudsepp, Terje
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7830431/
https://www.ncbi.nlm.nih.gov/pubmed/33467186
http://dx.doi.org/10.3390/genes12010105
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author Jevit, Matthew J.
Davis, Brian W.
Castaneda, Caitlin
Hillhouse, Andrew
Juras, Rytis
Trifonov, Vladimir A.
Tibary, Ahmed
Pereira, Jorge C.
Ferguson-Smith, Malcolm A.
Raudsepp, Terje
author_facet Jevit, Matthew J.
Davis, Brian W.
Castaneda, Caitlin
Hillhouse, Andrew
Juras, Rytis
Trifonov, Vladimir A.
Tibary, Ahmed
Pereira, Jorge C.
Ferguson-Smith, Malcolm A.
Raudsepp, Terje
author_sort Jevit, Matthew J.
collection PubMed
description The unique evolutionary dynamics and complex structure make the Y chromosome the most diverse and least understood region in the mammalian genome, despite its undisputable role in sex determination, development, and male fertility. Here we present the first contig-level annotated draft assembly for the alpaca (Vicugna pacos) Y chromosome based on hybrid assembly of short- and long-read sequence data of flow-sorted Y. The latter was also used for cDNA selection providing Y-enriched testis transcriptome for annotation. The final assembly of 8.22 Mb comprised 4.5 Mb of male specific Y (MSY) and 3.7 Mb of the pseudoautosomal region. In MSY, we annotated 15 X-degenerate genes and two novel transcripts, but no transposed sequences. Two MSY genes, HSFY and RBMY, are multicopy. The pseudoautosomal boundary is located between SHROOM2 and HSFY. Comparative analysis shows that the small and cytogenetically distinct alpaca Y shares most of MSY sequences with the larger dromedary and Bactrian camel Y chromosomes. Most of alpaca X-degenerate genes are also shared with other mammalian MSYs, though WWC3Y is Y-specific only in alpaca/camels and the horse. The partial alpaca Y assembly is a starting point for further expansion and will have applications in the study of camelid populations and male biology.
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spelling pubmed-78304312021-01-26 An 8.22 Mb Assembly and Annotation of the Alpaca (Vicugna pacos) Y Chromosome Jevit, Matthew J. Davis, Brian W. Castaneda, Caitlin Hillhouse, Andrew Juras, Rytis Trifonov, Vladimir A. Tibary, Ahmed Pereira, Jorge C. Ferguson-Smith, Malcolm A. Raudsepp, Terje Genes (Basel) Article The unique evolutionary dynamics and complex structure make the Y chromosome the most diverse and least understood region in the mammalian genome, despite its undisputable role in sex determination, development, and male fertility. Here we present the first contig-level annotated draft assembly for the alpaca (Vicugna pacos) Y chromosome based on hybrid assembly of short- and long-read sequence data of flow-sorted Y. The latter was also used for cDNA selection providing Y-enriched testis transcriptome for annotation. The final assembly of 8.22 Mb comprised 4.5 Mb of male specific Y (MSY) and 3.7 Mb of the pseudoautosomal region. In MSY, we annotated 15 X-degenerate genes and two novel transcripts, but no transposed sequences. Two MSY genes, HSFY and RBMY, are multicopy. The pseudoautosomal boundary is located between SHROOM2 and HSFY. Comparative analysis shows that the small and cytogenetically distinct alpaca Y shares most of MSY sequences with the larger dromedary and Bactrian camel Y chromosomes. Most of alpaca X-degenerate genes are also shared with other mammalian MSYs, though WWC3Y is Y-specific only in alpaca/camels and the horse. The partial alpaca Y assembly is a starting point for further expansion and will have applications in the study of camelid populations and male biology. MDPI 2021-01-16 /pmc/articles/PMC7830431/ /pubmed/33467186 http://dx.doi.org/10.3390/genes12010105 Text en © 2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Jevit, Matthew J.
Davis, Brian W.
Castaneda, Caitlin
Hillhouse, Andrew
Juras, Rytis
Trifonov, Vladimir A.
Tibary, Ahmed
Pereira, Jorge C.
Ferguson-Smith, Malcolm A.
Raudsepp, Terje
An 8.22 Mb Assembly and Annotation of the Alpaca (Vicugna pacos) Y Chromosome
title An 8.22 Mb Assembly and Annotation of the Alpaca (Vicugna pacos) Y Chromosome
title_full An 8.22 Mb Assembly and Annotation of the Alpaca (Vicugna pacos) Y Chromosome
title_fullStr An 8.22 Mb Assembly and Annotation of the Alpaca (Vicugna pacos) Y Chromosome
title_full_unstemmed An 8.22 Mb Assembly and Annotation of the Alpaca (Vicugna pacos) Y Chromosome
title_short An 8.22 Mb Assembly and Annotation of the Alpaca (Vicugna pacos) Y Chromosome
title_sort 8.22 mb assembly and annotation of the alpaca (vicugna pacos) y chromosome
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7830431/
https://www.ncbi.nlm.nih.gov/pubmed/33467186
http://dx.doi.org/10.3390/genes12010105
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