Transcriptome analysis of head kidney in grass carp and discovery of immune-related genes
<p>Abstract</p> <p>Background</p> <p>Grass carp (<it>Ctenopharyngodon idella</it>) is one of the most economically important freshwater fish, but its production is often affected by diseases that cause serious economic losses. To date, no good breeding varie...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2012-07-01
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| Series: | BMC Veterinary Research |
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| Online Access: | http://www.biomedcentral.com/1746-6148/8/108 |
| _version_ | 1818760299681939456 |
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| author | Chen Jin Li Cai Huang Rong Du Fukuan Liao Lanjie Zhu Zuoyan Wang Yaping |
| author_facet | Chen Jin Li Cai Huang Rong Du Fukuan Liao Lanjie Zhu Zuoyan Wang Yaping |
| author_sort | Chen Jin |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Grass carp (<it>Ctenopharyngodon idella</it>) is one of the most economically important freshwater fish, but its production is often affected by diseases that cause serious economic losses. To date, no good breeding varieties have been obtained using the oriented cultivation technique. The ability to identify disease resistance genes in grass carp is important to cultivate disease-resistant varieties of grass carp.</p> <p>Results</p> <p>In this study, we constructed a non-normalized cDNA library of head kidney in grass carp, and, after clustering and assembly, we obtained 3,027 high-quality unigenes. Solexa sequencing was used to generate sequence tags from the transcriptomes of the head kidney in grass carp before and after grass carp reovirus (GCRV) infection. After processing, we obtained 22,144 tags that were differentially expressed by more than 2-fold between the uninfected and infected groups. 679 of the differentially expressed tags (3.1%) mapped to 483 of the unigenes (16.0%). The up-regulated and down-regulated unigenes were annotated using gene ontology terms; 16 were annotated as immune-related and 42 were of unknown function having no matches to any of the sequences in the databases that were used in the similarity searches. Semi-quantitative RT-PCR revealed four unknown unigenes that showed significant responses to the viral infection. Based on domain structure predictions, one of these sequences was found to encode a protein that contained two transmembrane domains and, therefore, may be a transmembrane protein. Here, we proposed that this novel unigene may encode a virus receptor or a protein that mediates the immune signalling pathway at the cell surface.</p> <p>Conclusion</p> <p>This study enriches the molecular basis data of grass carp and further confirms that, based on fish tissue-specific EST databases, transcriptome analysis is an effective route to discover novel functional genes.</p> |
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| institution | Directory Open Access Journal |
| issn | 1746-6148 |
| language | English |
| last_indexed | 2024-12-18T06:56:25Z |
| publishDate | 2012-07-01 |
| publisher | BMC |
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| series | BMC Veterinary Research |
| spelling | doaj.art-d7e7eb523ead4fe484358765843253212022-12-21T21:17:10ZengBMCBMC Veterinary Research1746-61482012-07-018110810.1186/1746-6148-8-108Transcriptome analysis of head kidney in grass carp and discovery of immune-related genesChen JinLi CaiHuang RongDu FukuanLiao LanjieZhu ZuoyanWang Yaping<p>Abstract</p> <p>Background</p> <p>Grass carp (<it>Ctenopharyngodon idella</it>) is one of the most economically important freshwater fish, but its production is often affected by diseases that cause serious economic losses. To date, no good breeding varieties have been obtained using the oriented cultivation technique. The ability to identify disease resistance genes in grass carp is important to cultivate disease-resistant varieties of grass carp.</p> <p>Results</p> <p>In this study, we constructed a non-normalized cDNA library of head kidney in grass carp, and, after clustering and assembly, we obtained 3,027 high-quality unigenes. Solexa sequencing was used to generate sequence tags from the transcriptomes of the head kidney in grass carp before and after grass carp reovirus (GCRV) infection. After processing, we obtained 22,144 tags that were differentially expressed by more than 2-fold between the uninfected and infected groups. 679 of the differentially expressed tags (3.1%) mapped to 483 of the unigenes (16.0%). The up-regulated and down-regulated unigenes were annotated using gene ontology terms; 16 were annotated as immune-related and 42 were of unknown function having no matches to any of the sequences in the databases that were used in the similarity searches. Semi-quantitative RT-PCR revealed four unknown unigenes that showed significant responses to the viral infection. Based on domain structure predictions, one of these sequences was found to encode a protein that contained two transmembrane domains and, therefore, may be a transmembrane protein. Here, we proposed that this novel unigene may encode a virus receptor or a protein that mediates the immune signalling pathway at the cell surface.</p> <p>Conclusion</p> <p>This study enriches the molecular basis data of grass carp and further confirms that, based on fish tissue-specific EST databases, transcriptome analysis is an effective route to discover novel functional genes.</p>http://www.biomedcentral.com/1746-6148/8/108Grass carpHead kidneycDNAESTImmune-related gene |
| spellingShingle | Chen Jin Li Cai Huang Rong Du Fukuan Liao Lanjie Zhu Zuoyan Wang Yaping Transcriptome analysis of head kidney in grass carp and discovery of immune-related genes BMC Veterinary Research Grass carp Head kidney cDNA EST Immune-related gene |
| title | Transcriptome analysis of head kidney in grass carp and discovery of immune-related genes |
| title_full | Transcriptome analysis of head kidney in grass carp and discovery of immune-related genes |
| title_fullStr | Transcriptome analysis of head kidney in grass carp and discovery of immune-related genes |
| title_full_unstemmed | Transcriptome analysis of head kidney in grass carp and discovery of immune-related genes |
| title_short | Transcriptome analysis of head kidney in grass carp and discovery of immune-related genes |
| title_sort | transcriptome analysis of head kidney in grass carp and discovery of immune related genes |
| topic | Grass carp Head kidney cDNA EST Immune-related gene |
| url | http://www.biomedcentral.com/1746-6148/8/108 |
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