1
|
Chen L, Zhou Z, Zhou Z, Yang J, Deng Y, Bai Y, Pu F, Zhou T, Xu P. Chromosome-level assembly and gene annotation of Decapterus maruadsi genome using Nanopore and Hi-C technologies. Sci Data 2024; 11:69. [PMID: 38218740 PMCID: PMC10787795 DOI: 10.1038/s41597-024-02912-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 01/02/2024] [Indexed: 01/15/2024] Open
Abstract
Decapterus maruadsi is one of the representative offshore fish in the Western Pacific. Since the last century, it has become a commercially valuable marine fishery species in the Western Pacific region. Despite its high economic value, there is still a lack of high-quality reference genome of D. maruadsi in germplasm resource evaluation research. Here we report a chromosome-level reference genome of D. maruadsi based on Nanopore sequencing and Hi-C technologies. The whole genome was assembled through 169 contigs with a total length of 723.69 Mb and a contig N50 length of 24.67 Mb. By chromosome scaffolding, 23 chromosomes with a total length of 713.58 Mb were constructed. In addition, a total of 199.49 Mb repetitive elements, 33,515 protein-coding genes, and 6,431 ncRNAs were annotated in the reference genome. This reference genome of D. maruadsi will provide a solid theoretical basis not only for the subsequent development of genomic resources of D. maruadsi but also for the formulation of policies related to the protection of D. maruadsi.
Collapse
Affiliation(s)
- Longyu Chen
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Zhixiong Zhou
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Zhiyin Zhou
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Junyi Yang
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Yacheng Deng
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Yulin Bai
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Fei Pu
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Tao Zhou
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Peng Xu
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China.
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China.
| |
Collapse
|