The Oyster Genome Project – the first for an aquaculture species in China

Guofan Zhang(1), Ximing Guo(1,3), Li Li(1), Fei Xu(1), Haigang Qi(1), Linsheng Song(1), Xiao Liu(1), Baozhong Liu(1), Huayong Que(1), Bin Liu(1), Peizhou Cheng(1), Qi Wu(1), Linlin Zhang(1), Shaozhong Wang(1), Hougang Wu(2), Shihuan Wang(2), Jun Wang(4), Ruiqiang Li(4), Zhenmin Bao(5), Qi Li(5), Ziniu Yu(6), Rongqing Zhang(7), Dennis Hedgecock(8), Patrick M.Gaffney(9)

(1) Institute of Oceanology, Chinese Academy of Sciences. 7 Nanhai Road, Qingdao, Shandong 266071, China
(2) Dalian Zhangzidao Fishery Group Co., Ltd. 26 Renmin Road, Dalian, Liaoning 116001, China
(3) Haskin Shellfish Research Laboratory, Rutgers University. 6959 Miller Avenue, Port Norris, NJ 08349, USA
(4) Beijing Genomics Institute-Shenzhen. 10F, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
(5) China Ocean University. 238 Songling Road, Qingdao, Shandong 266100, China
(6) Institute of South China Sea, Chinese Academy of Sciences. 164 West Xingang Road, Guangzhou, 510301, China
(7) Tsinghua University. Haidian District, Beijing 100084, China
(8) Department of Biological Sciences, University of Southern California. 3616 Trousdale Pkwy, Los Angeles, CA 90089, USA
(9) College of Marine and Earth Studies, University of Delaware. 700 Pilot town Road, Lewes, DE 19958, USA

China is a global leader in aquaculture and accounts for about 70% of the world production. Aquaculture is important for China’s rural economy and as a food source for the people. The scale and importance of the Chinese aquaculture industry have not been matched with significant investments in advanced breeding technologies, and genomic research on aquaculture species remains limited. Most of the aquaculture species have not been domesticated, and genome-based breeding technologies are needed for rapid genetic improvement. The advent of new sequencing technologies has opened new opportunities for aquaculture genomics.

To demonstrate the potential of new sequencing technologies in aquaculture genomics, the Institute of Oceanology of Chinese Academy of Sciences (IOCAS) and the Beijing Genomics Institute (BGI), in collaboration with the international Oyster Genome Consortium (OGC), have initiated a genome project for the Pacific oyster Crassostrea gigas. Oysters are marine bivalve molluscs and important aquaculture species. Worldwide aquaculture production of oysters amounted to 4.6 million metric tons in 2006, second only to that of cyprinids. Oysters are also ecologically important species. As filter-feeders and reef-builders, they play a key role in energy transfer and providing habitats for other organisms. China is especially rich in oyster resources. It has at least 17 oyster species distributed along its coast, and several of them are economically and ecologically important. China, with an annual production of 3.8 million tons, is the largest producer of farmed oysters, and oyster farming is the largest sector of China’s mariculture industry. Oysters are the most studied members of the second largest phylum of Metazoan, the Mollusca, for which genomic information remains scarce, and the genome sequence of an oyster should contribute significantly to comparative genomics and evolutionary biology. The Pacific oyster is selected for the genome project because of its relatively small genome size (824 Mbp), its significance as a major aquaculture species in China and many other countries and the amount of genomic resources available. The goal of the project is to produce a draft genome sequence of the Pacific oyster to support gene discovery, evolutionary studies and genome-based breeding. The project uses a combination of traditional Sanger sequencing and next generation sequencing technologies: Solexa and 454 for deep coverage and Sanger sequencing of fosmid ends for connectivity. An inbred oyster is used to minimize potential problems with highly polymorphism which is typical for marine invertebrates. Sequencing has begun at BGI, and we will present a preliminary analysis at the meeting.

Keywords: Pacific oyster, genome sequence, comparative genomics, evolution, aquaculture, genome-based breeding