Progress of the Shrimp Genomic Sequencing Project

Penaeid shrimp are most economically important marine aquaculture species in China and also in the world. Genetic information, especially whole genome sequence is necessary to better understand the biological essence, and to promote the domestication and genetically improvement in shrimp. However, because its genome is large and complex in structure, estimated approximately 80% repetitive sequences, it is very difficult to sequence and good assemble. Both genomes of the Pacific white shrimpLitopenaeus vannamei and Chinese shrimp Fenneropenaeus chinensis have been sequenced and assembled for many years funded by grants of the National High Technology Research and Development Program of China. Using Next Generation Sequencing (NGS) technologies, different insert-size pair-end and mate-pair Illumina shotgun libraries were constructed, a total of 828GB and 530GB data were generated, covered 318X and 280X genome size of the two important cultured species of shrimp respectively. PacBio single molecule sequencing was adopted also and more than 70 GB data were generated for assisting assembling in each genome. A set of assembly methods were developed to solve the problems brought by high repetition and heterozygous character of shrimp genome, two preliminary genome drafts were constructed. A set of strategies have been utilized to facilitate assembly. The L. vannamei genome scaffold N50 was up to 123.98Kb; and the assembled F. chinensis genome scaffold N50 reached 154.2Kb. Paired BAC-end sequencing was conducted, 28,000 BAC ends were obtained. A high-density genetic map of L. vannamei has been developed, on which 6,359 SNP markers were mapped to the 44 linkage groups spanning 4,243 cM. Two dozen of transcriptomes were sequenced and all reads were assembled into 117,539 and 188,201 unigenes in L. vannameiand F. chinensis, at least 95% unigenes were mapped into the assembled genomes. Annotation of the genome of both shrimp is going on. These genome sequences and resource will facilitate the understanding of shrimp and crustacean genome, and should improve the genetic breeding in shrimp.