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Frontiers in genetics
2019;10 1340.

High-Quality Genome Assembly of Reveals Its Unique Genome Evolution.

Boping Tang, Zhongkai Wang, Qiuning Liu, Huabin Zhang, Senhao Jiang, Xinzheng Li, Zhengfei Wang, Yue Sun, Zhongli Sha, Hui Jiang, Xugan Wu, Yandong Ren, Haorong Li, Fujun Xuan, Baoming Ge, Wei Jiang, Shusheng She, Hongying Sun, Qiang Qiu, Wen Wang, Qun Wang, Gaofeng Qiu, Daizhen Zhang, Yongxin Li
Author Information
  1. Boping Tang: Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University, Yancheng, China.
  2. Zhongkai Wang: Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, China.
  3. Qiuning Liu: Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University, Yancheng, China.
  4. Huabin Zhang: Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University, Yancheng, China.
  5. Senhao Jiang: Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University, Yancheng, China.
  6. Xinzheng Li: Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.
  7. Zhengfei Wang: Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University, Yancheng, China.
  8. Yue Sun: Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University, Yancheng, China.
  9. Zhongli Sha: Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.
  10. Hui Jiang: National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, China.
  11. Xugan Wu: Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China.
  12. Yandong Ren: Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, China.
  13. Haorong Li: Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, China.
  14. Fujun Xuan: Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University, Yancheng, China.
  15. Baoming Ge: Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University, Yancheng, China.
  16. Wei Jiang: Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.
  17. Shusheng She: China-Hong Kong Ecology Consultant Company, Hong Kong, Hong Kong.
  18. Hongying Sun: College of Life Sciences, Nanjing Normal University, Nanjing, China.
  19. Qiang Qiu: Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, China.
  20. Wen Wang: Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, China.
  21. Qun Wang: Department of Biology, School of Life Science, East China Normal University, Shanghai, China.
  22. Gaofeng Qiu: Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China.
  23. Daizhen Zhang: Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University, Yancheng, China.
  24. Yongxin Li: Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, China.
PMID: 32010195 DOI: 10.3389/fgene.2019.01340

Abstract

As an important freshwater aquaculture species in China, the Chinese mitten crab () has high economic and nutritional value. However, limited genomic information is currently available for studying its basic development and genetic diversity. Here, we performed whole-genome sequencing on Oxford Nanopore Technologies Limited's platform using promethION. The assembled size of genome was approximately 1.27 Gb, which is close to the estimated size (1.19 Gb). Furthermore, based on assessment using Benchmarking Universal Single-Copy Orthologs (BUSCO) (Simao et al., 2015), 94.00% of the expected eukaryotic genes were completely present in the genome assembly. In addition, repetitive sequences accounted for ~61.42% of the assembled genome, and 22,619 protein-coding genes were annotated. Comparative genomics analysis demonstrated that the Chinese mitten crab diverged from ~373.6 million years ago, with a faster evolution rate than shrimp. We anticipate that the annotated high-quality genome of will promote research on its basic development and evolution and make substantial contributions to comparative genomic analyses of crustaceans.

Keywords

Eriocheir japonica sinensis crab evolution genome assembly and annotation nanopore

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Journal Article
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