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. Application of RNA-Seq can provide a far more precise measurement on levels of transcripts and their isoforms. RNA-Seq 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. In the transcriptome, a total of 64,188,426 Illumina reads, including 31,685,758 reads from the latent infection group and 32,502,668 reads from the acute infection group, were generated and assembled into 46,676 unigenes (mean length: 676 bp; range: 200-15,094 bp). Among which, 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 further 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 18 ºC (Group W) and 25 ºC(Group WT). About 6,421 differentially expressed genes (DEGs) were obtained. 4689 DEGs were down-regulated in Group WT and the other 1,732 DEGs were up-regulated, of which 173 were WSSV genes. According to the Gene Ontology analysis, the DEGs were involved in various biological processes, such as immune system process, metabolic process, energy production, organelle and cytoskeleton organization, cell cycle, signal transduction, death, cell adhesion, response to stimulus and so on, suggesting that WSSV propagation after temperature rising had a comprehensive influences on the host. Almost all the DEGs related to energy production were up-regulated in Group WT, suggesting an increased energy need and a boosted energy production; DEGs related to cell cycle were down-regulated in Group WT, suggesting that the host cell proliferation was inhibited. Through analyzing the DEGs in the glycometabolism pathways, a reduced glycometabolism level through the tricarboxylic acid cycle pathway (TCA) in Group WT were observed. Phosphopentose epimerase and xylose isomerase, involved in pentose phosphate pathway (PPP), were up-regulated in Group WT, suggesting a glycol-metabolism pathway transition from TCA to PPP. The above data provide useful information for understanding the mechanism for the breakout of shrimp virus disease.