Transcriptome Analysis of Pacific White Shrimp (Litopenaeus vannamei) Hepatopancreas in Response to Taura Syndrome Virus (TSV) Experimental Infection

Abstract

BackgroundThe Pacific white shrimp, Litopenaeus vannamei, is a worldwide cultured crustacean species with important commercial value. Over the last two decades, Taura syndrome virus (TSV) has seriously threatened the shrimp aquaculture industry in the Western Hemisphere. To better understand the interaction between shrimp immune and TSV, we performed a transcriptome analysis in the hepatopancreas of L. vannamei challenged with TSV, using the 454 pyrosequencing (Roche) technology.Methodology/Principal FindingsWe obtained 126919 and 102181 high-quality reads from TSV-infected and non-infected (control) L. vannamei cDNA libraries, respectively. The overall de novo assembly of cDNA sequence data generated 15004 unigenes, with an average length of 507 bp. Based on BLASTX search (E-value <10−5) against NR, Swissprot, GO, COG and KEGG databases, 10425 unigenes (69.50% of all unigenes) were annotated with gene descriptions, gene ontology terms, or metabolic pathways. In addition, we identified 770 microsatellites and designed 497 sets of primers. Comparative genomic analysis revealed that 1311 genes differentially expressed in the infected shrimp compared to the controls, including 559 up- and 752 down- regulated genes. Among the differentially expressed genes, several are involved in various animal immune functions, such as antiviral, antimicrobial, proteases, protease inhibitors, signal transduction, transcriptional control, cell death and cell adhesion.Conclusions/SignificanceThis study provides valuable information on shrimp gene activities against TSV infection. Results can contribute to the in-depth study of candidate genes in shrimp immunity, and improves our current understanding of this host-virus interaction. In addition, the large amount of transcripts reported in this study provide a rich source for identification of novel genes in shrimp.

Consumption of Ulva clathrata as a dietary supplement stimulates immune and lipid metabolism genes in Pacific white shrimp Litopenaeus vannamei

“…An average 87 % of differentially expressed transcripts were annotated with the different databases; nevertheless, 13 % had low sequence homology with the sequences that were already known through public databases. These data matched with the aforementioned data presented by Zeng et al (2013) and by Chen et al (2013b). In the same way, they obtained 80 % similarity with currently reported transcripts.…”

“…Such studies have had the objective to understand the organism's response related to nutritional changes and diet quality, in an attempt to improve insect diets (Yocum et al 2006;Alaux et al 2011;Zou et al 2013). In crustaceans, massive parallel sequencing has been employed to identify genes related to immune response, after inoculation with a virus Zeng et al 2013;Chen et al 2013a;Sookruksawong et al 2013); however, this new tool has not been used in nutritional studies. The present study has as an objective to use next-generation sequencing and bioinformatic techniques in order to obtain information about the L. vannamei transcriptome when these shrimp are fed a live U. clathrata as a dietary supplement, in order to find an explanation at the molecular level of the benefits of eating seaweed, i.e., genes that change their expression level and metabolic pathways in which these genes are involved.…”

Molecular cloning, characterization, and expression of Rab5B, Rab6A, and Rab7 from Litopenaeus vannamei (Penaeidae)

“…Cloning of the Rab5B, Rab6A, and Rab7 proteins from L. vannamei Partial cDNA sequences that are homologous to Drosophila Rab5B, Rab6A, and Rab7 were retrieved from the sequenced L. vannamei transcriptome data, which was previously completed in our research group (Zeng et al, 2013). The full length cDNA sequences of shrimp Rab5B, Rab6A, and Rab7 were then obtained using the rapid amplification of cDNA ends (RACE) method.…”

Identification of highly expressed host microRNAs that respond to white spot syndrome virus infection in the Pacific white shrimp Litopenaeus vannamei (Penaeidae)

“…The WSSV suspension was prepared from frozen (-80°C) WSSV-infected L. vannamei as described previously (James et al, 2010). The WSSV concentration was determined in our previous experiment, in which real-time quantitative PCR methods and reference samples containing gradient concentrations of WSSV were used (Zeng et al, 2013).…”