Ziniu Yu, Yang Zhang and Zhiming Xiang

South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Address: 164 West Xingang Road, Guangzhou 510301, P. R. China.

e-mail: carlzyu@scsio.ac.cn

Key words: Crassostrea hongkongensis,Genome, Assembly, Annotation

Hong Kong oyster Crassostrea hongkongensis, a member of the phylum Mollusca, is a dominant oyster species along the coast waters of South China Sea, with a long cultivation history and has been a popular seafood with a high market demand. The identification of genes related to various physiological processes in this oyster might enhance our understanding of reproduction, possibly contributing to the production of high-quality seeds and also help understand the underlying molecular mechanisms of the traits related to immunity and stress adaptation, which may provide a basis for better strain development in aquaculture.

A total of 147.25 gigabases (Gb) of raw reads were obtained from genome mapping of the Hong Kong oysters by PE125 format of high throughput sequencing on Illumina HiSeq 2500 platform. The estimated final genome assembly (714.88 Mb), covering about 98.20% of the estimated genome size, was found to be composed of 20.34 Kb of contig N50 and 618.24 Kb of scaffold N50 respectively. A total number of 35,624 genes were predicted; of which 90.84% were annotated on the basis of available genomic databases and 1,223 gene families were found to be specific to C. hongkongensis. A total of 154 tRNA, 83 rRNA, 807 miRNA, 2,607 pseudogenes and 415.71 Mb repetitive sequences were predicted. Based on comparisons with other all studies of C. hongkongensis with other oysters and non-mollusk species it could be concluded that oyster genome might not have undergone large-scale genome duplication events. In addition, the molecular basis of hemolytic phagocytosis and shell formation were also analyzed in genomic level. In conclusion, we report the first draft genome sequence, assembly and annotation of C. hongkongensis. The assembled genome will provide a valuable resource for the study of essential physiological processes, phylogeny and evolution among this Hong Kong oyster.