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URL: https://dx.doi.org/10.17504/protocols.io.ssxeefn

Authors: Changwei Shao, Chang Li, Na Wang, Yating Qin, Wenteng Xu, Qun Liu, Qian Zhou, Yong Zhao, Xihong Li, Shanshan Liu, Xiaowu Chen, Shahid Mahboob, Xin Liu, Songlin Chen

Group: GigaScience Press, BGI

Summary: Background: The spotted sea bass (Lateolabrax maculatus) is a valuable commercial fish that is widely cultured in China. While analyses using molecular markers and population genetics have been conducted, genomic resources are lacking.Finding: Here, we report a chromosome-scale assembly of the spotted sea bass genome by high-depth genome sequencing, assembly and annotation. The genome scale was 0.62 Gb with contig and scaffold N50 length to be 31 Kb and 1,040 Kb, respectively. Hi-C scaffolding of the genome resulted in 24 pseudochromosomes containing 77.68% of the total assembled sequences. A total of 132.38Mb repeat sequences were detected, accounting for 20.73% of the assemble genome. 22,015 protein-coding genes were predicted, of which 96.52% were homologous to proteins in various databases. In addition, we constructed a phylogenetic tree using 1,586 single-copy gene families and identified 125 unique gene families in the spotted sea bass genome.Conclusions: We assembled a spotted sea bass genome, which will be a valuable genomic resource to understand the biology of the spotted sea bass, and will also lead to the development of molecular breeding techniques to generate spotted sea bass with better economical traits.

Affiliations: Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China. Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China., BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China; BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China; BGI-Shenzhen, Shenzhen, 518083, China., Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China. Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China., BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China; BGI-Shenzhen, Shenzhen, 518083, China., Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China., BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China, Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China. Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China., BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China, Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China., BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China; BGI-Shenzhen, Shenzhen, 518083, China., Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China., Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia; Department of Zoology, GC University, Faisalabad, Pakistan., BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China; BGI-Shenzhen, Shenzhen, 518083, China., Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China. Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.

Version: 1

Publication Date: 2018

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