Transcriptome Analysis on Chinese Shrimp <em>Fenneropenaeus chinensis</em> during WSSV Acute Infection

Previous studies have discovered a lot of immune-related genes responding to white spot syndrome virus (WSSV) infection in crustacean. However, little information is available in relation to underlying mechanisms of host responses during the WSSV acute infection stage in naturally infected shrimp. In this study, we employed next-generation sequencing and bioinformatic techniques to observe the transcriptome differences of the shrimp between latent infection stage and acute infection stage. 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). Approximately 24,000 peptides were predicted and classified based on homology searches, gene ontology, clusters of orthologous groups of proteins, and biological pathway mapping. 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. The anti-bacterially proPO-activating cascade was firstly uncovered to be probably participated in antiviral process. These genes contain not only members playing function in host defense against WSSV, but also genes utilized by WSSV for its rapid proliferation. In addition, the transcriptome data provides detail information for identifying novel genes in absence of the genome database of shrimp.既往研究已在甲壳动物（crustacean）中发现了大量响应白斑综合征病毒（white spot syndrome virus, WSSV）感染的免疫相关基因。然而，针对自然感染虾类在WSSV急性感染阶段宿主应答的潜在分子机制，目前相关研究仍较为匮乏。本研究采用二代测序（next-generation sequencing）与生物信息学技术，分析比较了虾类潜伏感染阶段与急性感染阶段的转录组差异。本研究共产出64,188,426条Illumina测序读段（reads），其中潜伏感染组与急性感染组分别包含31,685,758条与32,502,668条读段；经组装后共得到46,676条单基因簇（unigene），平均长度为676 bp，长度范围为200~15,094 bp。研究人员通过同源序列比对、基因本体（gene ontology, GO）注释、直系同源蛋白簇（clusters of orthologous groups of proteins, COG）分类以及生物学通路注释，共预测得到约24,000条肽段并完成功能分类。在此基础上，共鉴定得到805个差异表达基因（differentially expressed genes, DEGs），并根据其潜在功能分为11个功能类群。研究发现，从潜伏感染阶段向急性感染阶段转变的过程中，虾类的Toll通路、IMD通路、Ras激活的内吞过程、RNA干扰（RNA interference, RNAi）通路以及抗脂多糖因子（anti-lipopolysaccharide factors, ALFs）等诸多基因均被激活。本研究首次发现，原本参与抗菌过程的酚氧化酶原激活级联反应（proPO-activating cascade）可能也参与了抗病毒免疫应答。这些基因不仅包含参与宿主抗WSSV免疫防御的功能分子，同时也包含被WSSV利用以实现快速增殖的宿主基因。此外，由于虾类目前尚无完整的基因组数据库，本研究产出的转录组数据可为新型功能基因的挖掘提供详实的参考信息。