The length statistics of all scaffolds are presented in Figure 1. Scaffold annotation was achieved through BLASTN similarity searches figure 2 against the zebrafish RefSeq mRNA database. This analysis revealed that 10,502 of the 26,313 scaffolds shared homology with zebrafish genes when a cutoff E value of 1e 05 was used. Scaffolds were clustered if two or more query sequences were annotated to the same zebrafish gene. Ultimately, 5715 unigenes were obtained. Scaffolds that did not display any similarity to zebrafish genes were further searched against the nonredundant database, and 2501 unigenes were obtained after clustering. In total, 8216 unigenes were identified in the transcriptome of the large yellow croaker. The remaining 13,102 scaffolds failed to match proteins in the nr database and therefore represented potentially novel genes.

Gene ontology analysis of these genes was per formed using the web based Database for Annotation, Visualization, and Integrated Discovery. Among the 8216 unigenes, DAVID had func tional annotation for 5590 genes. The DAVID functional annotation analysis for GO is summarized in Table 1. Sequences with GO terms corresponding to the cellular component group fell into 14 subcategories, molecular function into 16 subcategories, and biologi cal process into 31 subcategories. The largest subcate gory found in the cellular component group was cell part, which comprised 98. 8% of the genes in this subca tegory. In the molecular function and biological pro cess categories, nucleotide binding and primary metabolic process were the most abundant GO terms, making up 22.

4% and 50. 2% of each subcategory, respectively. To identify the biological pathways that are active in the large yellow croaker, we mapped the 8216 genes to canonical signaling pathways found in the Kyoto Ency clopedia of Genes and Genomes. A total of 3094 genes of the large yellow croaker transcriptome were mapped to KEGG, and 20 statistically remarkable categories are listed in Table 2. The mitogen activated protein kinase signaling pathway, neurotrophin signaling pathway, and chemo kine signaling pathway were identified as statistically significant. In fact, 47 genes were found to be related to the MAPK pathway. Other major immune pathways, such as those mediated by the T cell receptor and B cell receptor, were also statistically significant.

Global changes in gene expression upon A. hydrophila infection To characterize the immune response of the large yel low croaker to bacterial infection, two DeepSAGE libraries were constructed using mRNA from spleens injected with A. hydrophila or 0. 9% NaCl. After removal Drug_discovery of the low quality tags, adaptor tags, and one copynum ber tag, a total of 4,841,402 and 5,395,715 clean tags were obtained from the two libraries with 100,107 and 108,572 unique nucleotide sequences, respectively.