grass carp DGE
Transcriptome analysis of head kidney in grass carp and discovery of immune-related genes
Background: Grass carp (Ctenopharyngodon idella) is one of the most economically important freshwater fish, but its production is often affected by diseases that cause serious economic losses. So far it has not been one case of good breeding species of oriented cultivation. The ability to identify disease resistance genes in grass carp is important to cultivate disease-resistant varieties of grass carp.   Results: In this study, we constructed a non-normalized cDNA library of head kidney in grass carp, and obtained 3,027 high-quality unigenes. Then 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 differential 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 a significant response 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. We have proposed that this novel unigene may encode a virus receptor or a protein that mediates the immune signaling pathway at the cell surface.  Conclusion: 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.
Background: Grass carp (Ctenopharyngodon idella) is one of the most economically important freshwater fish, but its production is often affected by diseases that cause serious economic losses. So far it has not been one case of good breeding species of oriented cultivation. The ability to identify disease resistance genes in grass carp is important to cultivate disease-resistant varieties of grass carp.   Results: In this study, we constructed a non-normalized cDNA library of head kidney in grass carp, and obtained 3,027 high-quality unigenes. Then 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 differential 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 a significant response 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. We have proposed that this novel unigene may encode a virus receptor or a protein that mediates the immune signaling pathway at the cell surface.  Conclusion: 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.