Assembly of the poorly differentiated Verasper variegatus W chromosome by different sequencing technologies
Abstract The assembly of W and Y chromosomes poses significant challenges in vertebrate genome sequencing and assembly. Here, we successfully assembled the W chromosome of Verasper variegatus with a length of 20.48 Mb by combining population and PacBio HiFi sequencing data. It was identified as a yo...
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| Format: | Article |
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Nature Portfolio
2023-12-01
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| Series: | Scientific Data |
| Online Access: | https://doi.org/10.1038/s41597-023-02790-z |
| _version_ | 1797388525426966528 |
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| author | Xi-wen Xu Pengchuan Sun Chengbin Gao Weiwei Zheng Songlin Chen |
| author_facet | Xi-wen Xu Pengchuan Sun Chengbin Gao Weiwei Zheng Songlin Chen |
| author_sort | Xi-wen Xu |
| collection | DOAJ |
| description | Abstract The assembly of W and Y chromosomes poses significant challenges in vertebrate genome sequencing and assembly. Here, we successfully assembled the W chromosome of Verasper variegatus with a length of 20.48 Mb by combining population and PacBio HiFi sequencing data. It was identified as a young sex chromosome and showed signs of expansion in repetitive sequences. The major component of the expansion was Ty3/Gypsy. The ancestral Osteichthyes karyotype consists of 24 protochromosomes. The sex chromosomes in four Pleuronectiformes species derived from a pair of homologous protochromosomes resulting from a whole-genome duplication event in teleost fish, yet with different sex-determination systems. V. variegatus and Cynoglossus semilaevis adhere to the ZZ/ZW system, while Hippoglossus stenolepis and H. hippoglossus follow the XX/XY system. Interestingly, V. variegatus and H. hippoglossus derived from one protochromosome, while C. semilaevis and H. stenolepis derived from another protochromosome. Our study provides valuable insights into the evolution of sex chromosomes in flatfish and sheds light on the important role of whole-genome duplication in shaping the evolution of sex chromosomes. |
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| id | doaj.art-2b265d5e1c1d44229b14318f36e3a69e |
| institution | Directory Open Access Journal |
| issn | 2052-4463 |
| language | English |
| last_indexed | 2024-03-08T22:42:07Z |
| publishDate | 2023-12-01 |
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| spelling | doaj.art-2b265d5e1c1d44229b14318f36e3a69e2023-12-17T12:06:23ZengNature PortfolioScientific Data2052-44632023-12-011011810.1038/s41597-023-02790-zAssembly of the poorly differentiated Verasper variegatus W chromosome by different sequencing technologiesXi-wen Xu0Pengchuan Sun1Chengbin Gao2Weiwei Zheng3Songlin Chen4State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery SciencesKey Laboratory for Bio-resources and Eco-environment & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Sciences, Sichuan UniversityState Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery SciencesState Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery SciencesState Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery SciencesAbstract The assembly of W and Y chromosomes poses significant challenges in vertebrate genome sequencing and assembly. Here, we successfully assembled the W chromosome of Verasper variegatus with a length of 20.48 Mb by combining population and PacBio HiFi sequencing data. It was identified as a young sex chromosome and showed signs of expansion in repetitive sequences. The major component of the expansion was Ty3/Gypsy. The ancestral Osteichthyes karyotype consists of 24 protochromosomes. The sex chromosomes in four Pleuronectiformes species derived from a pair of homologous protochromosomes resulting from a whole-genome duplication event in teleost fish, yet with different sex-determination systems. V. variegatus and Cynoglossus semilaevis adhere to the ZZ/ZW system, while Hippoglossus stenolepis and H. hippoglossus follow the XX/XY system. Interestingly, V. variegatus and H. hippoglossus derived from one protochromosome, while C. semilaevis and H. stenolepis derived from another protochromosome. Our study provides valuable insights into the evolution of sex chromosomes in flatfish and sheds light on the important role of whole-genome duplication in shaping the evolution of sex chromosomes.https://doi.org/10.1038/s41597-023-02790-z |
| spellingShingle | Xi-wen Xu Pengchuan Sun Chengbin Gao Weiwei Zheng Songlin Chen Assembly of the poorly differentiated Verasper variegatus W chromosome by different sequencing technologies Scientific Data |
| title | Assembly of the poorly differentiated Verasper variegatus W chromosome by different sequencing technologies |
| title_full | Assembly of the poorly differentiated Verasper variegatus W chromosome by different sequencing technologies |
| title_fullStr | Assembly of the poorly differentiated Verasper variegatus W chromosome by different sequencing technologies |
| title_full_unstemmed | Assembly of the poorly differentiated Verasper variegatus W chromosome by different sequencing technologies |
| title_short | Assembly of the poorly differentiated Verasper variegatus W chromosome by different sequencing technologies |
| title_sort | assembly of the poorly differentiated verasper variegatus w chromosome by different sequencing technologies |
| url | https://doi.org/10.1038/s41597-023-02790-z |
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