The oyster genome reveals stress adaptation and complexity of shell formation

Guofan Zhang (), Xiaodong Fang, Ximing Guo (), Li Li, Ruibang Luo, Fei Xu, Pengcheng Yang, Linlin Zhang, Xiaotong Wang, Haigang Qi, Zhiqiang Xiong, Huayong Que, Yinlong Xie, Peter W. H. Holland, Jordi Paps, Yabing Zhu, Fucun Wu, Yuanxin Chen, Jiafeng Wang, Chunfang Peng, Jie Meng, Lan Yang, Jun Liu, Bo Wen, Na Zhang, Zhiyong Huang, Qihui Zhu, Yue Feng, Andrew Mount, Dennis Hedgecock, Zhe Xu, Yunjie Liu, Tomislav Domazet-Lošo, Yishuai Du, Xiaoqing Sun, Shoudu Zhang, Binghang Liu, Peizhou Cheng, Xuanting Jiang, Juan Li, Dingding Fan, Wei Wang, Wenjing Fu, Tong Wang, Bo Wang, Jibiao Zhang, Zhiyu Peng, Yingxiang Li, Na Li, Jinpeng Wang, Maoshan Chen, Yan He, Fengji Tan, Xiaorui Song, Qiumei Zheng, Ronglian Huang, Hailong Yang, Xuedi Du, Li Chen, Mei Yang, Patrick M. Gaffney, Shan Wang, Longhai Luo, Zhicai She, Yao Ming, Wen Huang, Shu Zhang, Baoyu Huang, Yong Zhang, Tao Qu, Peixiang Ni, Guoying Miao, Junyi Wang, Qiang Wang, Christian E. W. Steinberg, Haiyan Wang, Ning Li, Lumin Qian, Guojie Zhang, Yingrui Li, Huanming Yang, Xiao Liu, Jian Wang, Ye Yin () and Jun Wang ()
Additional contact information
Guofan Zhang: Institute of Oceanology
Xiaodong Fang: BGI-Shenzhen
Ximing Guo: Haskin Shellfish Research Laboratory, Institute of Marine and Coastal Sciences, Rutgers University
Li Li: Institute of Oceanology
Ruibang Luo: BGI-Shenzhen
Fei Xu: Institute of Oceanology
Pengcheng Yang: BGI-Shenzhen
Linlin Zhang: Institute of Oceanology
Xiaotong Wang: Institute of Oceanology
Haigang Qi: Institute of Oceanology
Zhiqiang Xiong: BGI-Shenzhen
Huayong Que: Institute of Oceanology
Yinlong Xie: BGI-Shenzhen
Peter W. H. Holland: University of Oxford, Oxford OX1 3PS, UK
Jordi Paps: University of Oxford, Oxford OX1 3PS, UK
Yabing Zhu: BGI-Shenzhen
Fucun Wu: Institute of Oceanology
Yuanxin Chen: BGI-Shenzhen
Jiafeng Wang: Institute of Oceanology
Chunfang Peng: BGI-Shenzhen
Jie Meng: Institute of Oceanology
Lan Yang: BGI-Shenzhen
Jun Liu: Institute of Oceanology
Bo Wen: BGI-Shenzhen
Na Zhang: Institute of Oceanology
Zhiyong Huang: BGI-Shenzhen
Qihui Zhu: Institute of Oceanology
Yue Feng: BGI-Shenzhen
Andrew Mount: Clemson University
Dennis Hedgecock: University of Southern California
Zhe Xu: Atlantic Cape Community College
Yunjie Liu: BGI-Shenzhen
Tomislav Domazet-Lošo: Laboratory of Evolutionary Genetics, Ruđer Bošković Institute, Bijenička cesta 54, P.P. 180, HR-10002, Zagreb, Croatia
Yishuai Du: Institute of Oceanology
Xiaoqing Sun: BGI-Shenzhen
Shoudu Zhang: Institute of Oceanology
Binghang Liu: BGI-Shenzhen
Peizhou Cheng: Institute of Oceanology
Xuanting Jiang: BGI-Shenzhen
Juan Li: Institute of Oceanology
Dingding Fan: BGI-Shenzhen
Wei Wang: Institute of Oceanology
Wenjing Fu: BGI-Shenzhen
Tong Wang: Institute of Oceanology
Bo Wang: BGI-Shenzhen
Jibiao Zhang: Institute of Oceanology
Zhiyu Peng: BGI-Shenzhen
Yingxiang Li: Institute of Oceanology
Na Li: BGI-Shenzhen
Jinpeng Wang: Institute of Oceanology
Maoshan Chen: BGI-Shenzhen
Yan He: Haskin Shellfish Research Laboratory, Institute of Marine and Coastal Sciences, Rutgers University
Fengji Tan: BGI-Shenzhen
Xiaorui Song: Institute of Oceanology
Qiumei Zheng: BGI-Shenzhen
Ronglian Huang: Institute of Oceanology
Hailong Yang: BGI-Shenzhen
Xuedi Du: Institute of Oceanology
Li Chen: BGI-Shenzhen
Mei Yang: Institute of Oceanology
Patrick M. Gaffney: School of Marine Science and Policy, University of Delaware
Shan Wang: Haskin Shellfish Research Laboratory, Institute of Marine and Coastal Sciences, Rutgers University
Longhai Luo: BGI-Shenzhen
Zhicai She: Institute of Oceanology
Yao Ming: BGI-Shenzhen
Wen Huang: Institute of Oceanology
Shu Zhang: BGI-Shenzhen
Baoyu Huang: Institute of Oceanology
Yong Zhang: BGI-Shenzhen
Tao Qu: Institute of Oceanology
Peixiang Ni: BGI-Shenzhen
Guoying Miao: Institute of Oceanology
Junyi Wang: BGI-Shenzhen
Qiang Wang: Institute of Oceanology
Christian E. W. Steinberg: Institute of Biology, Humboldt Universität zu Berlin Arboretum, Späthstraße 80/81, 12437 Berlin, Germany
Haiyan Wang: Institute of Oceanology
Ning Li: BGI-Shenzhen
Lumin Qian: Haskin Shellfish Research Laboratory, Institute of Marine and Coastal Sciences, Rutgers University
Guojie Zhang: BGI-Shenzhen
Yingrui Li: BGI-Shenzhen
Huanming Yang: BGI-Shenzhen
Xiao Liu: Institute of Oceanology
Jian Wang: BGI-Shenzhen
Ye Yin: BGI-Shenzhen
Jun Wang: BGI-Shenzhen

Nature, 2012, vol. 490, issue 7418, 49-54

Abstract: Abstract The Pacific oyster Crassostrea gigas belongs to one of the most species-rich but genomically poorly explored phyla, the Mollusca. Here we report the sequencing and assembly of the oyster genome using short reads and a fosmid-pooling strategy, along with transcriptomes of development and stress response and the proteome of the shell. The oyster genome is highly polymorphic and rich in repetitive sequences, with some transposable elements still actively shaping variation. Transcriptome studies reveal an extensive set of genes responding to environmental stress. The expansion of genes coding for heat shock protein 70 and inhibitors of apoptosis is probably central to the oyster’s adaptation to sessile life in the highly stressful intertidal zone. Our analyses also show that shell formation in molluscs is more complex than currently understood and involves extensive participation of cells and their exosomes. The oyster genome sequence fills a void in our understanding of the Lophotrochozoa.

Date: 2012
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DOI: 10.1038/nature11413

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