GENOME SEQUENCING OF THE PACIFIC WHITE SHRIMP, Litopenaeus vannamei

The Pacific white shrimp Litopenaeus vannamei is one of the most economically important marine aquaculture species in the world and China. However, the shrimp aquaculture industry has been threatened seriously by depletion of the culture bloodstock and outbreaks of viral disease. Genetic information, especially whole genome sequence is necessary to understand the biological essence, and to promote the domestication and genetically improvement in shrimp. However, the research on shrimp genome is still very limited, since huge genome, the difficulties for DNA isolation and operation, the lack of physical maps. Thanks to the rapid development of bioinformatics and sequencing technologies, shrimp genome sequencing and annotation has become a possible work during the last five years.

Here we report genome sequencing of L. vannamei, using new generation sequencing technology (Illumina and Pacific Bioscience). The bioinformatics assembly is a tremendous challenge because of the approximately 80% repetitive sequences in the shrimp genome. Our current assembly consists of 145,117 scaffolds with an N50 scaffold length of 124Kb (assembled using 302x Illumina) which is estimated to cover appr. 81% of the L. vannamei genome. We are currently working on improving this assembly by adding 30x of PacBio data and 34,266 BAC ends to aid scaffolding and gap filling. Seven transcriptomes ware sequenced and all reads were assembled and clustered into 117,539 unigenes, about 95% unigenes from transcriptomes were mapped into L. vannamei assembled genome. In a parallel effort we are re-sequencing multiple L. vannamei strains to explore the genomic mechanisms of rapid growth and high resistance to viral, bacteria disease and hypoxia.

Availability of the L. vannamei genome will open up new fields in marine aquaculture genome research by providing novel insights into the comparative genomics, developmental biology and evolutionary genomics of the shrimp.