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High-quality genome assembly of Chinese shrimp (Fenneropenaeus chinensis) suggests genome contraction and adaptation to the environment
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  • Qiong Wang,
  • Xianyun Ren,
  • Ping Liu,
  • Jitao Li,
  • Jianjian Lv,
  • Jiajia Wang,
  • Haien Zhang,
  • Wei Wei,
  • Yuxin Zhou,
  • Yuying He,
  • Jian Li
Qiong Wang
Chinese Academy of Fishery Science Yellow Sea Fisheries Research Institute
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Xianyun Ren
Chinese Academy of Fishery Science Yellow Sea Fisheries Research Institute
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Ping Liu
Chinese Academy of Fishery Sciences
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Jitao Li
Chinese Academy of Fishery Sciences
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Jianjian Lv
Chinese Academy of Fishery Science Yellow Sea Fisheries Research Institute
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Jiajia Wang
Chinese Academy of Fishery Science Yellow Sea Fisheries Research Institute
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Haien Zhang
Chinese Academy of Fishery Science Yellow Sea Fisheries Research Institute
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Wei Wei
Chinese Academy of Fishery Science Yellow Sea Fisheries Research Institute
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Yuxin Zhou
Chinese Academy of Fishery Science Yellow Sea Fisheries Research Institute
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Yuying He
Chinese Academy of Fishery Sciences
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Jian Li
Chinese Academy of Fishery Sciences
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Abstract

A high-quality reference genome is necessary to determine the molecular mechanisms underlying important biological phenomena; therefore, in the present study, a chromosome-level genome assembly of the Chinese shrimp Fenneropenaeus chinensis was performed. Muscle of a male shrimp was sequenced using PacBio platform, and assembled by Hi-C technology. The assembled F. chinensis genome was 1,465.32 Mb with contig N50 of 472.84 Kb, including 57.73% repetitive sequences, and was anchored to 43 pseudochromosomes, with scaffold N50 of 36.87 Mb. In total, 25,026 protein-coding genes were predicted. The genome size of F. chinensis showed significant contraction in comparison with that of other penaeid species, which is likely related to migration observed in this species. However, the F. chinensis genome included several expanded gene families related to cellular processes and metabolic processes, and the contracted gene families were associated with virus infection process. The findings signify the adaptation of F. chinensis to the selection pressure of migration and cold environment. Furthermore, the selection signature analysis identified genes associated with metabolism, phototransduction, and nervous system in cultured shrimps when compared with wild population, indicating targeted, artificial selection of growth, vision, and behavior during domestication. The construction of the genome of F. chinensis provided valuable information for the further genetic mechanism analysis of important biological processes, and will facilitate the research of genetic changes during evolution.

Peer review status:UNDER REVIEW

24 Mar 2021Submitted to Molecular Ecology Resources
08 Apr 2021Submission Checks Completed
08 Apr 2021Assigned to Editor
09 Apr 2021Reviewer(s) Assigned
23 Apr 2021Review(s) Completed, Editorial Evaluation Pending
26 May 2021Editorial Decision: Revise Minor
10 Jun 2021Review(s) Completed, Editorial Evaluation Pending
10 Jun 20211st Revision Received
12 Jun 2021Reviewer(s) Assigned