Application of RNA-Seq to Clarifying the Immune Mechanism of Shrimp to WSSV Infection

RNA-Seq is an approach using deep-sequencing technologies for transcriptome profiling. It is more and more widely used in aquatic animal to clarify the molecular mechanism for reproduction, development and immunity. WSSV is the most dangerous pathogen which can result in 90 to 100% mortality of shrimp. Understanding the immune mechanism of shrimp to WSSV infection is necessary for developing effective strategy for virus disease control. In the present study, RNA-seq was used to analyze the transcriptomic differences of the shrimp Fenneropenaeus chinensis between latent infection stage and acute infection stage of WSSV. Through differentiation analysis, 805 differentially expressed genes were identified and categorized into 11 groups based on their possible function. Genes in the Toll and IMD pathways, the Ras-activated endocytosis process, the RNA interference pathway, anti-lipopolysaccharide factors and many other genes, were found to be activated in shrimp from latent infection stage to acute infection stage. In order to learn the mechnism how temperature variation led to the break out of white spot syndrome, RNA-Seq was used to analyze the differential transcription between WSSV challenged shrimp Exopalamon carincauda Holthuis cultured at different temperature. About 6,421 differentially expressed genes (DEGs) were obtained, and they were involved in various biological processes, such as immune system process, metabolic process, energy production, organelle and cytoskeleton organization, cell cycle, signal transduction,etc., suggesting that WSSV propagation after temperature rising had a comprehensive influences on the host. The above data provide useful information for understanding the mechanism for the breakout of shrimp virus disease.