Abstract
BackgroundWhite spot syndrome virus (WSSV) is a causative pathogen found in most shrimp farming areas of the world and causes large economic losses to the shrimp aquaculture. The mechanism underlying the molecular pathogenesis of the highly virulent WSSV remains unknown. To better understand the virus-host interactions at the molecular level, the transcriptome profiles in hemocytes of unchallenged and WSSV-challenged shrimp (Litopenaeus vannamei) were compared using a short-read deep sequencing method (Illumina).ResultsRNA-seq analysis generated more than 25.81 million clean pair end (PE) reads, which were assembled into 52,073 unigenes (mean size = 520 bp). Based on sequence similarity searches, 23,568 (45.3%) genes were identified, among which 6,562 and 7,822 unigenes were assigned to gene ontology (GO) categories and clusters of orthologous groups (COG), respectively. Searches in the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG) mapped 14,941 (63.4%) unigenes to 240 KEGG pathways. Among all the annotated unigenes, 1,179 were associated with immune-related genes. Digital gene expression (DGE) analysis revealed that the host transcriptome profile was slightly changed in the early infection (5 hours post injection) of the virus, while large transcriptional differences were identified in the late infection (48 hpi) of WSSV. The differentially expressed genes mainly involved in pattern recognition genes and some immune response factors. The results indicated that antiviral immune mechanisms were probably involved in the recognition of pathogen-associated molecular patterns.ConclusionsThis study provided a global survey of host gene activities against virus infection in a non-model organism, pacific white shrimp. Results can contribute to the in-depth study of candidate genes in white shrimp, and help to improve the current understanding of host-pathogen interactions.
Highlights
Pacific white shrimp (L. vannamei) is one of the locally cultured shrimp in China and plays a major role in the Chinese mariculture industry
Total RNAs of control and White spot syndrome virus (WSSV)-challenged shrimp were obtained from hemocytes by using TRIzol reagent (Gibco BRL) following the manufacturer’s instructions and treated with RNase free DNase I (Qiagen)
The Illumina sequencing method was used to analyze the transcriptome of L. vannamei challenged with WSSV. 52,073 unigenes were assembled by 25.81 million clean reads
Summary
Pacific white shrimp (L. vannamei) is one of the locally cultured shrimp in China and plays a major role in the Chinese mariculture industry. Outbreak of disease caused by WSSV becomes the major stumbling blocks in the development and sustainability of shrimp aquaculture. WSSV is a large dsDNA virus infecting crustaceans and is the most important viral pathogen of cultured shrimp worldwide [1,2,3,4]. Because of its rapid spread and high associated mortality rates, WSSV is an extremely virulent pathogen in shrimp culture. White spot syndrome virus (WSSV) is a causative pathogen found in most shrimp farming areas of the world and causes large economic losses to the shrimp aquaculture. To better understand the virus-host interactions at the molecular level, the transcriptome profiles in hemocytes of unchallenged and WSSV-challenged shrimp (Litopenaeus vannamei) were compared using a short-read deep sequencing method (Illumina)
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