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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

COG function classification of unigenes in the TSV-infected and non-infected Litopenaeus vannamei cDNA libraries.All putative proteins were aligned to the COG database and can be classified functionally into at least 25 molecular families.
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pone-0057515-g002: COG function classification of unigenes in the TSV-infected and non-infected Litopenaeus vannamei cDNA libraries.All putative proteins were aligned to the COG database and can be classified functionally into at least 25 molecular families.

Mentions: We also searched the annotated sequences for the genes involved in COG classification. Among the 25 COG categories, the cluster for ‘General function prediction only’ (15.388%) represented the largest group, followed by the ‘Posttranslational modification, protein turnover, chaperones’ (12.83%) and ‘Translation, ribosomal structure and biogenesis’ (7.227%) clusters (Figure 2).


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)

COG function classification of unigenes in the TSV-infected and non-infected Litopenaeus vannamei cDNA libraries.All putative proteins were aligned to the COG database and can be classified functionally into at least 25 molecular families.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0057515-g002: COG function classification of unigenes in the TSV-infected and non-infected Litopenaeus vannamei cDNA libraries.All putative proteins were aligned to the COG database and can be classified functionally into at least 25 molecular families.
Mentions: We also searched the annotated sequences for the genes involved in COG classification. Among the 25 COG categories, the cluster for ‘General function prediction only’ (15.388%) represented the largest group, followed by the ‘Posttranslational modification, protein turnover, chaperones’ (12.83%) and ‘Translation, ribosomal structure and biogenesis’ (7.227%) clusters (Figure 2).

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