Chromosome-level genome assembly of the mud carp (Cirrhinus molitorella) using PacBio HiFi and Hi-C sequencing
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.
Authors
- Lingzhao Fang (ORCID: https://orcid.org/0000-0003-1103-3679)
- Jian Zhao (ORCID: https://orcid.org/0000-0002-4416-7334)
- Qing Luo (ORCID: https://orcid.org/0000-0002-1574-936X)
- Kunci Chen (ORCID: https://orcid.org/0000-0001-5512-4893)
- Mi Ou (ORCID: https://orcid.org/0000-0002-3537-4446)
- Chenjing Zhu (ORCID: https://orcid.org/0000-0001-8798-6367)
- Shuzhan Fei (ORCID: https://orcid.org/0000-0001-6957-7404)
- Haiyang Liu (ORCID: https://orcid.org/0000-0001-8301-4595)
- Bingjie Li (ORCID: https://orcid.org/0000-0002-8528-1889)
- Huijuan Liu (ORCID: https://orcid.org/0000-0002-8801-4815)
- Xinping Zhu (ORCID: https://orcid.org/0000-0003-1948-9590)
- Tongxin Cui
- Jin Zhang (ORCID: https://orcid.org/0000-0003-3554-2996)
Institutions
- Ningbo University (CN)
- Roslin Institute (GB)
- Aarhus University (DK)
- Scotland's Rural College (GB)
- Zhejiang Ocean University (CN)
- Huaiyin Normal University (CN)
- Ministry of Agriculture and Rural Affairs (CN)
- Shanghai Ocean University (CN)
- Chinese Academy of Fishery Sciences (CN)
Publication Details
- Journal
- Scientific Data
- Published
- 2024-11-19
- DOI
- https://doi.org/10.1038/s41597-024-04075-5
- Citations
- 4
- Primary Topic
- Genomics and Phylogenetic Studies
- Type
- article
- Field-Weighted Citation Impact
- 0.94
Funders
- Government of Jiangsu Province
- Natural Science Foundation of Jiangsu Province
- Central Public-interest Scientific Institution Basal Research Fund, Chinese Academy of Fishery Sciences