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De novo sequencing and chromosomal-scale genome assembly of leopard coral grouper, Plectropomus leopardus
  • +9
  • QIAN ZHOU,
  • Xinyu Guo,
  • Yang Huang,
  • Haoyang GaoOrcid,
  • Hao Xu,
  • Shanshan Liu,
  • Weiwei Zheng,
  • Tianshi Zhang,
  • Changxu Tian,
  • Chunhua Zhu,
  • Haoran Lin,
  • Songlin Chen
QIAN ZHOU
Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences
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Xinyu Guo
BGI-Qingdao, BGI-Shenzhen
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Yang Huang
Guangdong Ocean University
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Haoyang Gao
Orcid
BGI-Qingdao, BGI-Shenzhen
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Hao Xu
Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences
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Shanshan Liu
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Weiwei Zheng
Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences
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Tianshi Zhang
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Changxu Tian
Guangdong Ocean University
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Chunhua Zhu
Guangdong Ocean University
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Haoran Lin
Sun Yat-Sen University
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Songlin Chen
Yellow Sea Fisheries Research Institute
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Peer review status:ACCEPTED

14 Apr 2020Submitted to Molecular Ecology Resources
29 Apr 2020Reviewer(s) Assigned
13 May 2020Review(s) Completed, Editorial Evaluation Pending
27 May 2020Editorial Decision: Revise Minor
29 May 2020Review(s) Completed, Editorial Evaluation Pending
29 May 20201st Revision Received
03 Jun 2020Editorial Decision: Accept

Abstract

The leopard coral grouper, Plectropomus leopardus, belonging to genus Plectropomus, family Epinephelinae, is a carnivorous coral reef fish widely distributing in the tropical and subtropical water of Indo-Pacific Oceans. Due to its appealing body appearance and delicious taste, P. leopardus has become a popular commercial fish for aquaculture in many countries. However, the lack of genomic and molecular resources for P. leopardus hinders its biological studies and genomic breeding programs. Here we report the de novo sequencing and assembly of P. leopardus genome using 10× Genomics and high-throughput chromosome conformation capture (Hi-C) technologies. Using 127.36 Gb 10× Genomics we generated a 902.90 Mb genome assembly with a contig and scaffold N50 of 31.8 Kb and 33.47 Mb, respectively. The scaffolds were clustered and oriented into 24 pseudo-chromosomes with 13.39 Gb valid Hi-C data. BUSCO analysis showed that 95.3% of the conserved single-copy genes were retrieved, indicating a good entirety of the assembly. We predicted 23,234 protein-coding genes, among which 96.5% were functional annotated. The P. leopardus genome provides a valuable genomic resource for genetics, evolutionary and biological studies of this species. Particularly, it is expected to benefit the development of genomic breeding programs in the farming industry.