Chromosome-level genome assembly and annotation of the gynogenetic large-scale loach (Paramisgurnus dabryanus)
Abstracts The large-scale loach (Paramisgurnus dabryanus; Cypriniformes: Cobitidae) is primarily distributed in East Asia. It is an important economic fish species characterized by fast growth, temperature-dependent sex determination and the ability to breathe air. Currently, molecular mechanism stu...
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Nature Portfolio
2025-01-01
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| Series: | Scientific Data |
| Online Access: | https://doi.org/10.1038/s41597-025-04498-8 |
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| author | Lei Zhang Wanting Zhang Yingyin Cheng Yutong Fang Xin Guan Ao Gong Yanxin Jiang You Duan Lei Huang Waqar Younas Yaping Wang Mijuan Shi Xiao-Qin Xia |
| author_facet | Lei Zhang Wanting Zhang Yingyin Cheng Yutong Fang Xin Guan Ao Gong Yanxin Jiang You Duan Lei Huang Waqar Younas Yaping Wang Mijuan Shi Xiao-Qin Xia |
| author_sort | Lei Zhang |
| collection | DOAJ |
| description | Abstracts The large-scale loach (Paramisgurnus dabryanus; Cypriniformes: Cobitidae) is primarily distributed in East Asia. It is an important economic fish species characterized by fast growth, temperature-dependent sex determination and the ability to breathe air. Currently, molecular mechanism studies related to some aspects such as sex determination, toxicology, feed nutrition, growth and genetic evolution have been conducted. However, the lack of a high-quality reference genome has hindered further research. In this study, we performed PacBio HiFi and Hi-C sequencing on a female (ZW) specimen and assembled the first high-quality chromosome-level genome of the large-scale loach. The assembled genome comprises 24 chromosomes, with a total length of 1.04 Gb, a scaffold N50 of 41.7 Mb, and a BUSCO completeness of 95.8%, including 28,311 protein-coding genes. These findings not only provide new insights into the genome structure of the large-scale loach but also establish a crucial reference point for omics studies and serve as an essential genomic resource for breeding programs in this species. |
| format | Article |
| id | doaj-art-e5efdcf7e50f4b39b009aaa8b257843a |
| institution | Kabale University |
| issn | 2052-4463 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Data |
| spelling | doaj-art-e5efdcf7e50f4b39b009aaa8b257843a2025-01-26T12:14:30ZengNature PortfolioScientific Data2052-44632025-01-011211910.1038/s41597-025-04498-8Chromosome-level genome assembly and annotation of the gynogenetic large-scale loach (Paramisgurnus dabryanus)Lei Zhang0Wanting Zhang1Yingyin Cheng2Yutong Fang3Xin Guan4Ao Gong5Yanxin Jiang6You Duan7Lei Huang8Waqar Younas9Yaping Wang10Mijuan Shi11Xiao-Qin Xia12Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Hubei Hongshan Laboratory, Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture and Rural Affairs, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of SciencesKey Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Hubei Hongshan Laboratory, Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture and Rural Affairs, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of SciencesKey Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Hubei Hongshan Laboratory, Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture and Rural Affairs, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of SciencesKey Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Hubei Hongshan Laboratory, Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture and Rural Affairs, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of SciencesKey Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Hubei Hongshan Laboratory, Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture and Rural Affairs, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of SciencesKey Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Hubei Hongshan Laboratory, Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture and Rural Affairs, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of SciencesHefei Bestspectra Medical Lab Co., Ltd., 2800 Chuangxin RoadThe Joint Laboratory for Lung Development and Related Diseases of West China Second University Hospital, Sichuan University and School of Life Sciences of Fudan University, West China Institute of Women and Children’s Health, West China Second University Hospital, Sichuan UniversityYancheng Agricultural CollegeKey Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Hubei Hongshan Laboratory, Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture and Rural Affairs, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of SciencesKey Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Hubei Hongshan Laboratory, Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture and Rural Affairs, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of SciencesKey Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Hubei Hongshan Laboratory, Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture and Rural Affairs, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of SciencesKey Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Hubei Hongshan Laboratory, Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture and Rural Affairs, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of SciencesAbstracts The large-scale loach (Paramisgurnus dabryanus; Cypriniformes: Cobitidae) is primarily distributed in East Asia. It is an important economic fish species characterized by fast growth, temperature-dependent sex determination and the ability to breathe air. Currently, molecular mechanism studies related to some aspects such as sex determination, toxicology, feed nutrition, growth and genetic evolution have been conducted. However, the lack of a high-quality reference genome has hindered further research. In this study, we performed PacBio HiFi and Hi-C sequencing on a female (ZW) specimen and assembled the first high-quality chromosome-level genome of the large-scale loach. The assembled genome comprises 24 chromosomes, with a total length of 1.04 Gb, a scaffold N50 of 41.7 Mb, and a BUSCO completeness of 95.8%, including 28,311 protein-coding genes. These findings not only provide new insights into the genome structure of the large-scale loach but also establish a crucial reference point for omics studies and serve as an essential genomic resource for breeding programs in this species.https://doi.org/10.1038/s41597-025-04498-8 |
| spellingShingle | Lei Zhang Wanting Zhang Yingyin Cheng Yutong Fang Xin Guan Ao Gong Yanxin Jiang You Duan Lei Huang Waqar Younas Yaping Wang Mijuan Shi Xiao-Qin Xia Chromosome-level genome assembly and annotation of the gynogenetic large-scale loach (Paramisgurnus dabryanus) Scientific Data |
| title | Chromosome-level genome assembly and annotation of the gynogenetic large-scale loach (Paramisgurnus dabryanus) |
| title_full | Chromosome-level genome assembly and annotation of the gynogenetic large-scale loach (Paramisgurnus dabryanus) |
| title_fullStr | Chromosome-level genome assembly and annotation of the gynogenetic large-scale loach (Paramisgurnus dabryanus) |
| title_full_unstemmed | Chromosome-level genome assembly and annotation of the gynogenetic large-scale loach (Paramisgurnus dabryanus) |
| title_short | Chromosome-level genome assembly and annotation of the gynogenetic large-scale loach (Paramisgurnus dabryanus) |
| title_sort | chromosome level genome assembly and annotation of the gynogenetic large scale loach paramisgurnus dabryanus |
| url | https://doi.org/10.1038/s41597-025-04498-8 |
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