%0 Journal Article
%T Transcriptome analysis of head kidney in grass carp and discovery of immune-related genes
%A Jin Chen
%A Cai Li
%A Rong Huang
%A Fukuan Du
%A Lanjie Liao
%A Zuoyan Zhu
%A Yaping Wang
%J BMC Veterinary Research
%D 2012
%I BioMed Central
%R 10.1186/1746-6148-8-108
%X 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.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.Grass carp (Ctenopharyngodon idella) is one of the most important freshwater fish, with fast growth, low cost of breeding, and delicious meat. It is widely distributed in China's major river systems. Grass carp is a farmed species that is easily affected by diseases induced by viruses and bacteria; this can cause tremendous economic losses. To date, no excellent breeding varieties have been obtained by the oriented cultivation technique. Because of the long breeding cycle (4¨C5£¿years), a hybrid breeding strategy is not feasib
%K Grass carp
%K Head kidney
%K cDNA
%K EST
%K Immune-related gene
%U http://www.biomedcentral.com/1746-6148/8/108