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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Nature Portfolio
2017-08-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-017-08476-y |
| _version_ | 1819036057242435584 |
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| 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 |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-12-21T07:59:28Z |
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| id | doaj.art-9d483180cc4e49a9bd67b7b67c0c6de4 |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-12-21T07:59:28Z |
| publishDate | 2017-08-01 |
| publisher | Nature Portfolio |
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| spelling | doaj.art-9d483180cc4e49a9bd67b7b67c0c6de42022-12-21T19:10:56ZengNature PortfolioScientific Reports2045-23222017-08-017111210.1038/s41598-017-08476-yComputational identification of Y-linked markers and genes in the grass carp genome by using a pool-and-sequence methodAidi Zhang0Rong Huang1Liangming Chen2Lv Xiong3Libo He4Yongming Li5Lanjie Liao6Zuoyan Zhu7Yaping Wang8State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of SciencesState Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of SciencesState Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of SciencesState Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of SciencesState Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of SciencesState Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of SciencesState Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of SciencesState Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of SciencesState Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of SciencesAbstract 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.https://doi.org/10.1038/s41598-017-08476-y |
| spellingShingle | 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 Scientific Reports |
| title | 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_short | 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 |
| url | https://doi.org/10.1038/s41598-017-08476-y |
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