Sequencing and de novo analysis of the hemocytes transcriptome in Litopenaeus vannamei response to white spot syndrome virus infection

• Published in: PloS one Vol. 8; no. 10; p. e76718
• Main Authors: Xue, Shuxia, Liu, Yichen, Zhang, Yichen, Sun, Yan, Geng, Xuyun, Sun, Jinsheng
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 18-10-2013; Public Library of Science (PLoS)
• Subjects: Animals; Antiviral agents; Aquaculture; Aquaculture industry; Arthropod Proteins - genetics; Arthropod Proteins - immunology; Comparative analysis; Disease prevention; Disease Resistance - genetics; Disease Resistance - immunology; Economic impact; Encyclopedias; Gene expression; Gene Ontology; Gene sequencing; Genes; Genomes; Genomics; Health aspects; Hemocytes; Hemocytes - immunology; Hemocytes - metabolism; Hemocytes - virology; Host-pathogen interactions; Host-Pathogen Interactions - immunology; Identification; Immune response; Immune system; Infections; Infectious diseases; Laboratories; Life sciences; Litopenaeus vannamei; Mortality; Palaemonetes pugio; Pathogenesis; Pathogens; Pattern recognition; Penaeidae - immunology; Penaeidae - metabolism; Penaeidae - virology; Penaeus monodon; Plant resistance; Reverse Transcriptase Polymerase Chain Reaction; Ribonucleic acid; RNA; Searching; Sequence Analysis, RNA - methods; Shellfish; Transcription; Transcriptome - genetics; Transcriptome - immunology; Virology; Virulence (Microbiology); Viruses; White spot syndrome; White spot syndrome virus 1 - immunology; White spot syndrome virus 1 - physiology; China
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0076718

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. 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).
RNA-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.
This 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.