Chromosome-level genome assembly of the mud carp (Cirrhinus molitorella) using PacBio HiFi and Hi-C sequencing
Abstract The mud carp (Cirrhinus molitorella) is an important economic farmed fish, mainly distributed in South China and Southeast Asia due to its strong adaptability and high yield. Despite its economic importance, the paucity of genomic information has constrained detailed genetic research and br...
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Nature Portfolio
2024-11-01
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| Series: | Scientific Data |
| Online Access: | https://doi.org/10.1038/s41597-024-04075-5 |
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| author | Haiyang Liu Tongxin Cui Huijuan Liu Jin Zhang Qing Luo Shuzhan Fei Kunci Chen Xinping Zhu Chunkun Zhu Bingjie Li Lingzhao Fang Jian Zhao Mi Ou |
| author_facet | Haiyang Liu Tongxin Cui Huijuan Liu Jin Zhang Qing Luo Shuzhan Fei Kunci Chen Xinping Zhu Chunkun Zhu Bingjie Li Lingzhao Fang Jian Zhao Mi Ou |
| author_sort | Haiyang Liu |
| collection | DOAJ |
| description | Abstract The mud carp (Cirrhinus molitorella) is an important economic farmed fish, mainly distributed in South China and Southeast Asia due to its strong adaptability and high yield. Despite its economic importance, the paucity of genomic information has constrained detailed genetic research and breeding efforts. In this study, we utilized PacBio HiFi long-read sequencing and Hi-C technologies to generate a meticulously assembled chromosome-level genome of the mud carp. This assembly spans 1,033.41 Mb, with an impressive 99.82% distributed across 25 chromosomes. The contig N50 and scaffold N50 are 33.29 Mb and 39.86 Mb, respectively. The completeness of the mud carp genome assembly is highlighted by a BUSCO score of 98.05%. We predict 25,865 protein-coding genes, with a BUSCO score of 96.54%, and functional annotations for 91.83% of these genes. Approximately 52.21% of the genome consists of repeat elements. This high-fidelity genome assembly is a vital resource for advancing molecular breeding, comparative genomics, and evolutionary studies of the mud carp and related species. |
| format | Article |
| id | doaj-art-19540b08d63a4ad386087b1f59382013 |
| institution | Kabale University |
| issn | 2052-4463 |
| language | English |
| publishDate | 2024-11-01 |
| publisher | Nature Portfolio |
| record_format | Article |
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| spelling | doaj-art-19540b08d63a4ad386087b1f593820132024-11-24T12:10:08ZengNature PortfolioScientific Data2052-44632024-11-011111910.1038/s41597-024-04075-5Chromosome-level genome assembly of the mud carp (Cirrhinus molitorella) using PacBio HiFi and Hi-C sequencingHaiyang Liu0Tongxin Cui1Huijuan Liu2Jin Zhang3Qing Luo4Shuzhan Fei5Kunci Chen6Xinping Zhu7Chunkun Zhu8Bingjie Li9Lingzhao Fang10Jian Zhao11Mi Ou12Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery SciencesKey Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery SciencesKey Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery SciencesKey Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery SciencesKey Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery SciencesKey Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery SciencesKey Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery SciencesKey Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery SciencesSchool of Life science, Huaiyin Normal UniversityAnimal and Veterinary Sciences, Scotland’s Rural College (SRUC), Roslin Institute Building, Easter BushCenter for Quantitative Genetics and Genomics, Aarhus UniversityKey Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery SciencesKey Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery SciencesAbstract The mud carp (Cirrhinus molitorella) is an important economic farmed fish, mainly distributed in South China and Southeast Asia due to its strong adaptability and high yield. Despite its economic importance, the paucity of genomic information has constrained detailed genetic research and breeding efforts. In this study, we utilized PacBio HiFi long-read sequencing and Hi-C technologies to generate a meticulously assembled chromosome-level genome of the mud carp. This assembly spans 1,033.41 Mb, with an impressive 99.82% distributed across 25 chromosomes. The contig N50 and scaffold N50 are 33.29 Mb and 39.86 Mb, respectively. The completeness of the mud carp genome assembly is highlighted by a BUSCO score of 98.05%. We predict 25,865 protein-coding genes, with a BUSCO score of 96.54%, and functional annotations for 91.83% of these genes. Approximately 52.21% of the genome consists of repeat elements. This high-fidelity genome assembly is a vital resource for advancing molecular breeding, comparative genomics, and evolutionary studies of the mud carp and related species.https://doi.org/10.1038/s41597-024-04075-5 |
| spellingShingle | Haiyang Liu Tongxin Cui Huijuan Liu Jin Zhang Qing Luo Shuzhan Fei Kunci Chen Xinping Zhu Chunkun Zhu Bingjie Li Lingzhao Fang Jian Zhao Mi Ou Chromosome-level genome assembly of the mud carp (Cirrhinus molitorella) using PacBio HiFi and Hi-C sequencing Scientific Data |
| title | Chromosome-level genome assembly of the mud carp (Cirrhinus molitorella) using PacBio HiFi and Hi-C sequencing |
| title_full | Chromosome-level genome assembly of the mud carp (Cirrhinus molitorella) using PacBio HiFi and Hi-C sequencing |
| title_fullStr | Chromosome-level genome assembly of the mud carp (Cirrhinus molitorella) using PacBio HiFi and Hi-C sequencing |
| title_full_unstemmed | Chromosome-level genome assembly of the mud carp (Cirrhinus molitorella) using PacBio HiFi and Hi-C sequencing |
| title_short | Chromosome-level genome assembly of the mud carp (Cirrhinus molitorella) using PacBio HiFi and Hi-C sequencing |
| title_sort | chromosome level genome assembly of the mud carp cirrhinus molitorella using pacbio hifi and hi c sequencing |
| url | https://doi.org/10.1038/s41597-024-04075-5 |
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