Chromosome-level genome assembly of black carp Mylopharyngodon piceus using Nanopore and Hi-C technologies
Abstract Black carp (Mylopharyngodon piceus) is one of the “four famous domestic fishes” in China and an important economic fish in freshwater aquaculture. A high-quality genome is essential for advancing future biological research and breeding programs for this species. In this study, we aimed to g...
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Nature Portfolio
2025-01-01
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| Series: | Scientific Data |
| Online Access: | https://doi.org/10.1038/s41597-025-04421-1 |
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| author | Yuxuan Zhang Yanwen Shao Xudong Liu Liang Zhong Zhaoyan Zhong Weiwei Zeng Jiping Zhang Wenlong Cai Runsheng Li |
| author_facet | Yuxuan Zhang Yanwen Shao Xudong Liu Liang Zhong Zhaoyan Zhong Weiwei Zeng Jiping Zhang Wenlong Cai Runsheng Li |
| author_sort | Yuxuan Zhang |
| collection | DOAJ |
| description | Abstract Black carp (Mylopharyngodon piceus) is one of the “four famous domestic fishes” in China and an important economic fish in freshwater aquaculture. A high-quality genome is essential for advancing future biological research and breeding programs for this species. In this study, we aimed to generate a high-quality chromosome-level genome assembly of black carp using Nanopore and Hi-C technologies. The final genome assembly was 848.70 Mb in length, with a contig N50 of 3.37 Mb and a scaffold N50 of 34.13 Mb. The genome was anchored onto 24 chromosomes by Hi-C technology. The BUSCO (Benchmarking Universal Single-Copy Orthologs) completeness score of the genome assembly is 97.6% when compared to the Actinopterygii_odb10 database. In total, 203.54 Mb of repeat sequences and 37,418 protein-coding genes were predicted in the genome assembly. Taken together, our study provides a chromosome-level genome assembly, which can serve as a valuable genetic resource to support further biological studies and breeding efforts of black carp. |
| format | Article |
| id | doaj-art-379c8b873c7f43949a85abeb7b75d2e3 |
| institution | Kabale University |
| issn | 2052-4463 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Data |
| spelling | doaj-art-379c8b873c7f43949a85abeb7b75d2e32025-01-26T12:14:44ZengNature PortfolioScientific Data2052-44632025-01-011211710.1038/s41597-025-04421-1Chromosome-level genome assembly of black carp Mylopharyngodon piceus using Nanopore and Hi-C technologiesYuxuan Zhang0Yanwen Shao1Xudong Liu2Liang Zhong3Zhaoyan Zhong4Weiwei Zeng5Jiping Zhang6Wenlong Cai7Runsheng Li8Department of Infectious Diseases and Public Health, City University of Hong KongDepartment of Infectious Diseases and Public Health, City University of Hong KongDepartment of Infectious Diseases and Public Health, City University of Hong KongDepartment of Infectious Diseases and Public Health, City University of Hong KongDepartment of Infectious Diseases and Public Health, City University of Hong KongSchool of Life Science and Engineering, Foshan UniversitySchool of Life Science and Engineering, Foshan UniversityDepartment of Infectious Diseases and Public Health, City University of Hong KongDepartment of Infectious Diseases and Public Health, City University of Hong KongAbstract Black carp (Mylopharyngodon piceus) is one of the “four famous domestic fishes” in China and an important economic fish in freshwater aquaculture. A high-quality genome is essential for advancing future biological research and breeding programs for this species. In this study, we aimed to generate a high-quality chromosome-level genome assembly of black carp using Nanopore and Hi-C technologies. The final genome assembly was 848.70 Mb in length, with a contig N50 of 3.37 Mb and a scaffold N50 of 34.13 Mb. The genome was anchored onto 24 chromosomes by Hi-C technology. The BUSCO (Benchmarking Universal Single-Copy Orthologs) completeness score of the genome assembly is 97.6% when compared to the Actinopterygii_odb10 database. In total, 203.54 Mb of repeat sequences and 37,418 protein-coding genes were predicted in the genome assembly. Taken together, our study provides a chromosome-level genome assembly, which can serve as a valuable genetic resource to support further biological studies and breeding efforts of black carp.https://doi.org/10.1038/s41597-025-04421-1 |
| spellingShingle | Yuxuan Zhang Yanwen Shao Xudong Liu Liang Zhong Zhaoyan Zhong Weiwei Zeng Jiping Zhang Wenlong Cai Runsheng Li Chromosome-level genome assembly of black carp Mylopharyngodon piceus using Nanopore and Hi-C technologies Scientific Data |
| title | Chromosome-level genome assembly of black carp Mylopharyngodon piceus using Nanopore and Hi-C technologies |
| title_full | Chromosome-level genome assembly of black carp Mylopharyngodon piceus using Nanopore and Hi-C technologies |
| title_fullStr | Chromosome-level genome assembly of black carp Mylopharyngodon piceus using Nanopore and Hi-C technologies |
| title_full_unstemmed | Chromosome-level genome assembly of black carp Mylopharyngodon piceus using Nanopore and Hi-C technologies |
| title_short | Chromosome-level genome assembly of black carp Mylopharyngodon piceus using Nanopore and Hi-C technologies |
| title_sort | chromosome level genome assembly of black carp mylopharyngodon piceus using nanopore and hi c technologies |
| url | https://doi.org/10.1038/s41597-025-04421-1 |
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