Transcriptome analysis of orange-spotted grouper (<it>Epinephelus coioides</it>) spleen in response to Singapore grouper iridovirus
<p>Abstract</p> <p>Background</p> <p>Orange-spotted grouper (<it>Epinephelus coioides</it>) is an economically important marine fish cultured in China and Southeast Asian countries. The emergence of infectious viral diseases, including iridovirus and betanod...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2011-11-01
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| Series: | BMC Genomics |
| Online Access: | http://www.biomedcentral.com/1471-2164/12/556 |
| _version_ | 1828288301666140160 |
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| author | Huang Youhua Huang Xiaohong Yan Yang Cai Jia Ouyang Zhengliang Cui Huachun Wang Peiran Qin Qiwei |
| author_facet | Huang Youhua Huang Xiaohong Yan Yang Cai Jia Ouyang Zhengliang Cui Huachun Wang Peiran Qin Qiwei |
| author_sort | Huang Youhua |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Orange-spotted grouper (<it>Epinephelus coioides</it>) is an economically important marine fish cultured in China and Southeast Asian countries. The emergence of infectious viral diseases, including iridovirus and betanodavirus, have severely affected food products based on this species, causing heavy economic losses. Limited available information on the genomics of <it>E. coioides </it>has hampered the understanding of the molecular mechanisms that underlie host-virus interactions. In this study, we used a 454 pyrosequencing method to investigate differentially-expressed genes in the spleen of the <it>E. coioides </it>infected with Singapore grouper iridovirus (SGIV).</p> <p>Results</p> <p>Using 454 pyrosequencing, we obtained abundant high-quality ESTs from two spleen-complementary DNA libraries which were constructed from SGIV-infected (V) and PBS-injected fish (used as a control: C). A total of 407,027 and 421,141 ESTs were produced in control and SGIV infected libraries, respectively. Among the assembled ESTs, 9,616 (C) and 10,426 (V) ESTs were successfully matched against known genes in the NCBI non-redundant (nr) database with a cut-off E-value above 10<sup>-5</sup>. Gene ontology (GO) analysis indicated that "cell part", "cellular process" and "binding" represented the largest category. Among the 25 clusters of orthologous group (COG) categories, the cluster for "translation, ribosomal structure and biogenesis" represented the largest group in the control (185 ESTs) and infected (172 ESTs) libraries. Further KEGG analysis revealed that pathways, including cellular metabolism and intracellular immune signaling, existed in the control and infected libraries. Comparative expression analysis indicated that certain genes associated with mitogen-activated protein kinase (MAPK), chemokine, toll-like receptor and RIG-I signaling pathway were alternated in response to SGIV infection. Moreover, changes in the pattern of gene expression were validated by qRT-PCR, including cytokines, cytokine receptors, and transcription factors, apoptosis-associated genes, and interferon related genes.</p> <p>Conclusion</p> <p>This study provided abundant ESTs that could contribute greatly to disclosing novel genes in marine fish. Furthermore, the alterations of predicted gene expression patterns reflected possible responses of these fish to the virus infection. Taken together, our data not only provided new information for identification of novel genes from marine vertebrates, but also shed new light on the understanding of defense mechanisms of marine fish to viral pathogens.</p> |
| first_indexed | 2024-04-13T10:02:07Z |
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| institution | Directory Open Access Journal |
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| language | English |
| last_indexed | 2024-04-13T10:02:07Z |
| publishDate | 2011-11-01 |
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| spelling | doaj.art-bb5d34ef85bd476bbcd51daee3d513672022-12-22T02:51:13ZengBMCBMC Genomics1471-21642011-11-0112155610.1186/1471-2164-12-556Transcriptome analysis of orange-spotted grouper (<it>Epinephelus coioides</it>) spleen in response to Singapore grouper iridovirusHuang YouhuaHuang XiaohongYan YangCai JiaOuyang ZhengliangCui HuachunWang PeiranQin Qiwei<p>Abstract</p> <p>Background</p> <p>Orange-spotted grouper (<it>Epinephelus coioides</it>) is an economically important marine fish cultured in China and Southeast Asian countries. The emergence of infectious viral diseases, including iridovirus and betanodavirus, have severely affected food products based on this species, causing heavy economic losses. Limited available information on the genomics of <it>E. coioides </it>has hampered the understanding of the molecular mechanisms that underlie host-virus interactions. In this study, we used a 454 pyrosequencing method to investigate differentially-expressed genes in the spleen of the <it>E. coioides </it>infected with Singapore grouper iridovirus (SGIV).</p> <p>Results</p> <p>Using 454 pyrosequencing, we obtained abundant high-quality ESTs from two spleen-complementary DNA libraries which were constructed from SGIV-infected (V) and PBS-injected fish (used as a control: C). A total of 407,027 and 421,141 ESTs were produced in control and SGIV infected libraries, respectively. Among the assembled ESTs, 9,616 (C) and 10,426 (V) ESTs were successfully matched against known genes in the NCBI non-redundant (nr) database with a cut-off E-value above 10<sup>-5</sup>. Gene ontology (GO) analysis indicated that "cell part", "cellular process" and "binding" represented the largest category. Among the 25 clusters of orthologous group (COG) categories, the cluster for "translation, ribosomal structure and biogenesis" represented the largest group in the control (185 ESTs) and infected (172 ESTs) libraries. Further KEGG analysis revealed that pathways, including cellular metabolism and intracellular immune signaling, existed in the control and infected libraries. Comparative expression analysis indicated that certain genes associated with mitogen-activated protein kinase (MAPK), chemokine, toll-like receptor and RIG-I signaling pathway were alternated in response to SGIV infection. Moreover, changes in the pattern of gene expression were validated by qRT-PCR, including cytokines, cytokine receptors, and transcription factors, apoptosis-associated genes, and interferon related genes.</p> <p>Conclusion</p> <p>This study provided abundant ESTs that could contribute greatly to disclosing novel genes in marine fish. Furthermore, the alterations of predicted gene expression patterns reflected possible responses of these fish to the virus infection. Taken together, our data not only provided new information for identification of novel genes from marine vertebrates, but also shed new light on the understanding of defense mechanisms of marine fish to viral pathogens.</p>http://www.biomedcentral.com/1471-2164/12/556 |
| spellingShingle | Huang Youhua Huang Xiaohong Yan Yang Cai Jia Ouyang Zhengliang Cui Huachun Wang Peiran Qin Qiwei Transcriptome analysis of orange-spotted grouper (<it>Epinephelus coioides</it>) spleen in response to Singapore grouper iridovirus BMC Genomics |
| title | Transcriptome analysis of orange-spotted grouper (<it>Epinephelus coioides</it>) spleen in response to Singapore grouper iridovirus |
| title_full | Transcriptome analysis of orange-spotted grouper (<it>Epinephelus coioides</it>) spleen in response to Singapore grouper iridovirus |
| title_fullStr | Transcriptome analysis of orange-spotted grouper (<it>Epinephelus coioides</it>) spleen in response to Singapore grouper iridovirus |
| title_full_unstemmed | Transcriptome analysis of orange-spotted grouper (<it>Epinephelus coioides</it>) spleen in response to Singapore grouper iridovirus |
| title_short | Transcriptome analysis of orange-spotted grouper (<it>Epinephelus coioides</it>) spleen in response to Singapore grouper iridovirus |
| title_sort | transcriptome analysis of orange spotted grouper it epinephelus coioides it spleen in response to singapore grouper iridovirus |
| url | http://www.biomedcentral.com/1471-2164/12/556 |
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