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Chromosome-level genome assembly of burbot (Lota lota) provides insights into the evolutionary adaptations in freshwater
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  • Zhiqiang Han,
  • Manhong Liu,
  • Qi Liu,
  • Hao Zhai,
  • shijun xiao,
  • Tianxiang Gao
Zhiqiang Han
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Manhong Liu
Northeast Forestry University
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Qi Liu
Wuhan Gooalgene Technology Company
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Hao Zhai
Northeast Forestry University
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shijun xiao
Wuhan Gooalgene Technology Company
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Tianxiang Gao
Zhejiang Ocean University
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Abstract

The burbot (Lota lota) is the only member of the cod family (Gadidae) that is adapted solely to freshwater. This species shows the widest longitudinal range of freshwater fish in the world. The burbot is a good model for studies on adaptive genome evolution from marine to freshwater environment. However, no high-quality reference genome has been released. Here, the first chromosome-level genome of the burbot was constructed using PacBio long sequencing and Hi-C technology. A total of 95.24 Gb polished PacBio sequences were generated, and the preliminary genome assembly was 575.83 Mb in size with a contig N50 size of 2.15 Mb. The assembled sequences were anchored to 22 pseudo-chromosomes by using the Hi-C data. The final assembled genome after Hi-C correction was 575.92 Mb, with a contig N50 of 2.01 Mb and a scaffold N50 of 22.10 Mb. A total of 22,067 protein-coding genes were predicted, 94.82% of which were functionally annotated. Phylogenetic analyses indicated that burbot diverged with the Atlantic cod about 44.4 million years ago. In addition, 377 putative genes that appear to be under positive selection in burbot were identified. These positively selected genes might adapt to the freshwater environment. These genome data provide an invaluable resource for the ecological and evolutionary study of the order Gadiformes.

Peer review status:Published

18 Sep 2020Submitted to Molecular Ecology Resources
08 Oct 2020Submission Checks Completed
08 Oct 2020Assigned to Editor
28 Oct 2020Reviewer(s) Assigned
25 Nov 2020Review(s) Completed, Editorial Evaluation Pending
01 Dec 2020Editorial Decision: Revise Minor
10 Jan 2021Review(s) Completed, Editorial Evaluation Pending
10 Jan 20211st Revision Received
08 Feb 2021Editorial Decision: Revise Minor
02 Mar 2021Review(s) Completed, Editorial Evaluation Pending
02 Mar 20212nd Revision Received
11 Mar 2021Editorial Decision: Accept
17 Mar 2021Published in Molecular Ecology Resources. 10.1111/1755-0998.13382