Background

White spot syndrome (WSS) is a highly contagious viral disease of penaeid shrimp. The cumulative mortality of diseased shrimp can reach 100% within 3–10 days. Since its first outbreak in 1993, WSS has caused serious economic losses to the shrimp farming industry worldwide. The causative agent, white spot syndrome virus (WSSV), is an enveloped, non-occluded, rod-shaped virus that contains a circular, double-stranded DNA of about 300 kb. This virus has an extremely wide range of potential hosts, infecting not only shrimps, but also other decapods [1, 2]. WSSV infects most shrimp tissues and organs, and it replicates in the nuclei of infected cells. At the late stage of infection, either the nucleus or the whole cell disintegrates, leading to loss of cellular architecture. Both genomic and proteomic approaches have revealed the unique characteristics of the virus, and the virus has been erected as the type species of the new family of Nimaviridae [35].

Due to its serious impact on shrimp aquaculture, there is an urgent need to understand WSSV and to unveil the underlying mechanisms involved in WSSV pathogenesis in shrimp. Although considerable progress has been made in characterizing the virus, information on the host genes involved in WSSV pathogenesis is limited. To identify these host genes, one strategy is to isolate genes that are differentially expressed after WSSV infection. To that purpose, a variety of different approaches have been used, including an mRNA differential display technique [6], suppression subtractive hybridization [7], SSH and differential hybridization [8], cDNA microarrays [9, Functional annotation

Putative functions of the unique sequences were discovered by using BlastX to translate each nucleotide query sequence into all reading frames and then searching for matches in the NCBI non-redundant database. Significant hits (with E value < 10-10) in the NCBI nr database were followed up with protein function searches in the UniProt database [70], which provides value-added information reports for protein functions. The UniProt reports consist of Gene Ontology (GO) annotations that classify proteins by biological process, cellular component, and molecular function. Each unique sequence was tentatively assigned GO classification based on annotation of the single "best hit" match in UniProt. These data were then used to classify the corresponding genes according to their GO functions.

Expression analysis and statistical evaluation of EST occurrence

The unique sequences were considered to have increased abundance if they had a significantly greater number of hits (ie. more ESTs) in the WSSV-infected library compared to the normal library. Conversely, unique sequences were considered to have decreased abundance if they had significantly more hits in the normal library. The statistical significance of homologous ESTs with differential abundance was determined using Fisher's exact test [7173], which is widely used to evaluate 2 × 2 contingency tables. Fisher's exact test produces a significance value P ranging between 0 and 1, where a value close to 0 implies that there is a significant differential abundance of the gene or the annotated function between the normal and infected libraries. The significance of differential abundance genes with a P value smaller than 0.001 was considered "very strong". P values between 0.001 and 0.01, and between 0.01 and 0.05 were considered "strong" and "moderate", respectively.

Availability and requirements

Project name: Penaeus monodon Functional Genomics Database

Project home page: http://xbio.lifescience.ntu.edu.tw/pm/

Operating system: Platform independent

Programming language:PHP