Genome-Wide Survey of Litopenaeus vannamei, a Glimpse into the Genome Characterization of Penaeid Shrimp

Penaeid shrimps are representative taxa in crustacean and the most economically important marine aquaculture species in the world and China. However, the research on shrimp genome is still very limited. In this study, using BAC end sequencing, BAC clone sequencing, and Next Generation Sequencing, we analyzed the genome characterization of Pacific white shrimp Litopenaeus vannamei. A total of 7,812 BAC clones have been sequenced from the two ends of the inserts by Sanger method, 11,279 high quality BAC end sequences (BESs) were obtained, representing 0.18% of the L. vannamei haploid genome. Five BAC clones, total length of 429 kb, were sequenced and analyzed based on Sanger and Solexa sequencing to explore the genomic structure at the long DNA sequences level. And 40X genome coverage sequences were obtained to survey the L. vannamei genome by Solexa technology. Analysis of these data revealed that the L. vannamei genome is AT-rich (~60%) and that the primary repeats patterns were simple sequence repeats (SSRs) and low complexity sequences. Dinucleotide and hexanucleotide repeats were the most common SSR types in the BESs. The most abundant transposable element was gypsy, which may contribute to the generation of the large genome size of L. vannamei. By k-mer statistics, the estimation of the genome size is 2.6 Gb, the repetitive DNAs accounted for 86 % of the shrimp genome, and the genome heterozygosity rate was more than 9.8SNP/kb. Our results indicated shrimp possess of a complex genome, these data provide an important resource to better understand the genome characterization and improve sequencing and assembling penaeid shrimp genome.