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Transcriptome analysis of Pacific white shrimp (Litopenaeus vannamei) hepatopancreas in response to Taura syndrome Virus (TSV) experimental infection.

Zeng D, Chen X, Xie D, Zhao Y, Yang C, Li Y, Ma N, Peng M, Yang Q, Liao Z, Wang H, Chen X - PLoS ONE (2013)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Institute of Fisheries, Nanning, China.

ABSTRACT

Background: The 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 findings: We 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/significance: This 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.

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Related in: MedlinePlus

Comparison of the expression profiles of selected genes as determined by 454 sequencing (blue) and qRT-PCR (red).Target gene abbreviations are as follows: CATL - cathepsin L, AK - arginine kinase, FABP - fatty acids binding protein, ASF - alternative splicing factor, SDH - sorbitol dehydrogenase, HCS - hemocyanin.
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pone-0057515-g003: Comparison of the expression profiles of selected genes as determined by 454 sequencing (blue) and qRT-PCR (red).Target gene abbreviations are as follows: CATL - cathepsin L, AK - arginine kinase, FABP - fatty acids binding protein, ASF - alternative splicing factor, SDH - sorbitol dehydrogenase, HCS - hemocyanin.

Mentions: To validate our RNA-seq results, six differentially regulated genes with the different total transcript reads (range 44–1076) were selected for quantitative real time-PCR (qRT-PCR) analysis. The results indicate that the qRT-PCR analysis of the relatively high abundant genes (>500 reads) agrees well with the 454 sequencing analysis. For example, based on 454 sequencing analysis, cathepsin-L (CATL), arginine kinase (AK) and fatty acids binding protein (FABP) were differentially regulated 1.48, −1.26 and −2.53 log2-fold, respectively, and showed 1.25, −1.62 and −2.31 log2-fold changes, respectively in qRT-PCR analyses (Figure 3). However, the qRT-PCR analysis of the relatively low abundant genes (<500 reads), including alternative splicing factor (ASF), sorbitol dehydrogenase (SDH) and hemocyanin (HCS), do not match the 454 sequencing analysis perfectly, even if it shows similar trends in up- or down-regulation of genes analysised by 454 sequencing (Figure 3). Nevertheless, qRT-PCR analysis confirmed the change direction detected by the 454 sequencing analysis.


Transcriptome analysis of Pacific white shrimp (Litopenaeus vannamei) hepatopancreas in response to Taura syndrome Virus (TSV) experimental infection.

Zeng D, Chen X, Xie D, Zhao Y, Yang C, Li Y, Ma N, Peng M, Yang Q, Liao Z, Wang H, Chen X - PLoS ONE (2013)

Comparison of the expression profiles of selected genes as determined by 454 sequencing (blue) and qRT-PCR (red).Target gene abbreviations are as follows: CATL - cathepsin L, AK - arginine kinase, FABP - fatty acids binding protein, ASF - alternative splicing factor, SDH - sorbitol dehydrogenase, HCS - hemocyanin.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3585375&req=5

pone-0057515-g003: Comparison of the expression profiles of selected genes as determined by 454 sequencing (blue) and qRT-PCR (red).Target gene abbreviations are as follows: CATL - cathepsin L, AK - arginine kinase, FABP - fatty acids binding protein, ASF - alternative splicing factor, SDH - sorbitol dehydrogenase, HCS - hemocyanin.
Mentions: To validate our RNA-seq results, six differentially regulated genes with the different total transcript reads (range 44–1076) were selected for quantitative real time-PCR (qRT-PCR) analysis. The results indicate that the qRT-PCR analysis of the relatively high abundant genes (>500 reads) agrees well with the 454 sequencing analysis. For example, based on 454 sequencing analysis, cathepsin-L (CATL), arginine kinase (AK) and fatty acids binding protein (FABP) were differentially regulated 1.48, −1.26 and −2.53 log2-fold, respectively, and showed 1.25, −1.62 and −2.31 log2-fold changes, respectively in qRT-PCR analyses (Figure 3). However, the qRT-PCR analysis of the relatively low abundant genes (<500 reads), including alternative splicing factor (ASF), sorbitol dehydrogenase (SDH) and hemocyanin (HCS), do not match the 454 sequencing analysis perfectly, even if it shows similar trends in up- or down-regulation of genes analysised by 454 sequencing (Figure 3). Nevertheless, qRT-PCR analysis confirmed the change direction detected by the 454 sequencing analysis.

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Institute of Fisheries, Nanning, China.

ABSTRACT

Background: The 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 findings: We 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/significance: This 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.

Show MeSH
Related in: MedlinePlus