Computational identification of Y-linked markers and genes in the grass carp genome by using a pool-and-sequence method

Abstract The molecular analysis of sex in vertebrates is important, as it has the potential to provide vital information for theoretical and applied research alike. Teleost fish are the ancient vertebrates that present a broad sex chromosome system but lack differentiated sex chromosomes in most spe...

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Autores principales:	Aidi Zhang, Rong Huang, Liangming Chen, Lv Xiong, Libo He, Yongming Li, Lanjie Liao, Zuoyan Zhu, Yaping Wang
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/9d483180cc4e49a9bd67b7b67c0c6de4
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spelling	oai:doaj.org-article:9d483180cc4e49a9bd67b7b67c0c6de42021-12-02T15:06:00ZComputational identification of Y-linked markers and genes in the grass carp genome by using a pool-and-sequence method10.1038/s41598-017-08476-y2045-2322https://doaj.org/article/9d483180cc4e49a9bd67b7b67c0c6de42017-08-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-08476-yhttps://doaj.org/toc/2045-2322Abstract The molecular analysis of sex in vertebrates is important, as it has the potential to provide vital information for theoretical and applied research alike. Teleost fish are the ancient vertebrates that present a broad sex chromosome system but lack differentiated sex chromosomes in most species. Hence understanding the sex in fish would not only illuminate the sex determination evolution in vertebrates but also shed light on fish farming. In the present study, we used grass carp as a teleost fish model, studied the Y chromosome by using a pool-and-sequence strategy in combination with fragment-ratio method. In total, we identified five Y-linked scaffolds (totaling 347 Kb) and six Y-specific sequences that could be used as sex-specific markers, demonstrating the suitability of NGS-based re-sequencing of pooled DNAs for the identification of sex markers in fish. Moreover, 14 putative Y-linked genes were described for the first time. All the genes, except for un-y1, un-y2, and ubq-y, showed high similarity to their female homologs. RT-PCR revealed that ubq-y was only expressed in the male hypothalamus and pituitary. These findings provided an abundant resource for the Y chromosome of grass carp, and may help elucidate sex chromosome evolution in cyprinid fish.Aidi ZhangRong HuangLiangming ChenLv XiongLibo HeYongming LiLanjie LiaoZuoyan ZhuYaping WangNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-12 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Aidi Zhang Rong Huang Liangming Chen Lv Xiong Libo He Yongming Li Lanjie Liao Zuoyan Zhu Yaping Wang Computational identification of Y-linked markers and genes in the grass carp genome by using a pool-and-sequence method
description	Abstract The molecular analysis of sex in vertebrates is important, as it has the potential to provide vital information for theoretical and applied research alike. Teleost fish are the ancient vertebrates that present a broad sex chromosome system but lack differentiated sex chromosomes in most species. Hence understanding the sex in fish would not only illuminate the sex determination evolution in vertebrates but also shed light on fish farming. In the present study, we used grass carp as a teleost fish model, studied the Y chromosome by using a pool-and-sequence strategy in combination with fragment-ratio method. In total, we identified five Y-linked scaffolds (totaling 347 Kb) and six Y-specific sequences that could be used as sex-specific markers, demonstrating the suitability of NGS-based re-sequencing of pooled DNAs for the identification of sex markers in fish. Moreover, 14 putative Y-linked genes were described for the first time. All the genes, except for un-y1, un-y2, and ubq-y, showed high similarity to their female homologs. RT-PCR revealed that ubq-y was only expressed in the male hypothalamus and pituitary. These findings provided an abundant resource for the Y chromosome of grass carp, and may help elucidate sex chromosome evolution in cyprinid fish.
format	article
author	Aidi Zhang Rong Huang Liangming Chen Lv Xiong Libo He Yongming Li Lanjie Liao Zuoyan Zhu Yaping Wang
author_facet	Aidi Zhang Rong Huang Liangming Chen Lv Xiong Libo He Yongming Li Lanjie Liao Zuoyan Zhu Yaping Wang
author_sort	Aidi Zhang
title	Computational identification of Y-linked markers and genes in the grass carp genome by using a pool-and-sequence method
title_short	Computational identification of Y-linked markers and genes in the grass carp genome by using a pool-and-sequence method
title_full	Computational identification of Y-linked markers and genes in the grass carp genome by using a pool-and-sequence method
title_fullStr	Computational identification of Y-linked markers and genes in the grass carp genome by using a pool-and-sequence method
title_full_unstemmed	Computational identification of Y-linked markers and genes in the grass carp genome by using a pool-and-sequence method
title_sort	computational identification of y-linked markers and genes in the grass carp genome by using a pool-and-sequence method
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/9d483180cc4e49a9bd67b7b67c0c6de4
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Computational identification of Y-linked markers and genes in the grass carp genome by using a pool-and-sequence method

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