Identification of immune-relevant genes by expressed sequence tag analysis of head kidney from grass carp (Ctenopharyngodon idella)

Grass carp is the third largest aquaculture species in global production. However, genomic research of this species has been limited. To identify immune-related genes in grass carp, a normalized full-length cDNA library was constructed from head kidney tissues, and 6432 randomly selected clones were sequenced. 5289 high quality expressed sequence tags (EST) were generated and assembled into 2687 unigenes. Among them, 1585 unigenes showed significant similarity with known sequences in public databases, whereas the remaining 1102 unigenes appeared to be novel sequences with unknown functions. In particular, 136 immune-related genes were identified to encode immunoglobulins, FcRgamma, IFN-related proteins, various CD markers, MHCs, complements and other important immune-related factors; a majority of these genes are reported in grass carp for the first time. Sequence analysis indicated that grass carp has at least three subtypes of immunoglobulin light chains, namely L1, L2 and L3. Furthermore, FCRgamma was found to broadly express in different tissues. Our study constitutes the first EST analysis of lymphatic tissue in grass carp, and could pave the way for further research of immune-related genes and functional genomics in grass carp.