Advances on Genome Sequencing and Phylogenetic Analysis of Pacific White Shrimp Litopenaeus vannamei

Penaeid shrimps are most economically important marine aquaculture species in the world and China. 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, the research on shrimp genome is still very limited. Both genomes of the Pacific white shrimp Litopenaeus vannamei and Chinese shrimp Fenneropenaeus chinensis have been sequenced and assembled recently. Using Next Generation Sequencing (NGS) technologies, different insert-size pair-end and mate-pair shotgun libraries were constructed, a total of 786.13 GB and 475.17GB data were generated, covered 302 X and 250 X genome size of the two important cultured species of shrimp respectively. The bioinformatics assembly is a tremendous challenge because of the approximately 80% repetitive sequences in the shrimp genome. 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. Paired BAC-end sequencing was conducted and 28,000 BAC end were obtained. Five BAC clones were sequenced and analyzed based on Sanger and Illumina platform to explore the genomic structure at the long DNA sequences level. PacBio single molecule sequencing was attempted and 2.6 GB data were generated for assisting assembling. The construction of a shrimp physical map is in progress. Seven transcriptomes ware sequenced and all reads were assembled and clustered into 66,815 unigenes, about 95% unigenes from transcriptomes were mapped into L. vannamei assembled genome. Using present shrimp genome data, we analyzed the genome-wide horizontal gene transfer (HGT) events in L. vannamei, among them 14 HGT genes were identified. The analysis of genome characterization indicated shrimp possess of a large and complex genome. A set of strategies have been utilized to facilitate assembly, a high quality, available whole genome sequence draft can be obtained in the near future.

 Keywords: Genome, shrimp, NGS, genetic map, BAC

*Corresponding author. E-mail: jhxiang@qdio.ac.cn (Xiang JH) Phone No: + 86-532-82898568