Inflammation is a protective response that is implicated in bacterial enteritis and other fish diseases.The inflammatory mechanisms behind Aeromonas hydrophila infections in fish remain poorly understood. In this study, we performed a de novo grass carp transcriptome assembly using Illumina's Solexa sequencing technique. On this basis we carried out a comparative analysis of intestinal transcriptomes from A. hydrophila-challenged and physiological saline solution (PSS/mock) -challenged fish, and 315 genes were up-regulated and 234 were down-regulated in the intestines infected with A. hydrophila. The GO enrichment analysis indicated that the differentially expressed genes were enriched to 12, 4, and 8 GO terms in biological process, molecular function, and cellular component, respectively. A KEGG analysis showed that 549 DEGs were involved in 165 pathways. Moreover, 15 DEGs were selected for quantitative real-time PCR analysis to validate the RNA-seq data. The results confirmed the consistency of the expression levels between RNA-seq and qPCR data. In addition, a time-course analysis of the mRNA expression of 12 inflammatory genes further demonstrated that the intestinal inflammatory responses to A. hydrophila infection simultaneously modulated gene expression variations. The present study provides intestine-specific transcriptome data, allowing us to unravel the mechanisms of intestinal inflammation triggered by bacterial pathogens.The grass carp (Ctenopharyngodon idella) is an intensively cultured and economically important herbivorous fish species in China. In grass carp aquaculture, the fish are often infected by bacterial, viral and parasitic pathogens. Aeromonas hydrophila, a Gram-negative aquatic bacterium, is regarded as the major bacterial pathogen causing intestinal inflammation in animal taxa, including farmed fish 1-4 . A. hydrophila-induced enteritis is probably the most widespread disease in grass carp, especially under intensive rearing conditions, which results in huge economic losses annually due to reduced growth and high mortality rates [5][6][7] . The molecular mechanisms and pathways that regulate bacterial-induced inflammatory processes in humans and other mammalian species are relatively well understood [8][9][10] . In fish, several inflammation-related genes, including chemokine (C-X-C motif) ligand 2 (CXCL2) 11 , CXCL10 12 , cyclooxygenase-2 (COX-2) 13 , interleukin-1β (IL-1β ) 4,13,14 , IL-8 15,16 , IL-17A/F2 17 , and tumor necrosis factor (TNF)-α 13,18 , have already been identified and characterized with regard to their involvement in inflammatory responses to bacterial infections. However, the definitive mechanisms responsible for the bacterial-induced intestinal inflammation in fish are still unclear. Therefore, further studies are required to identify more molecular components that mediate inflammatory reactions in fish.In the past few years, transcriptome sequencing technology has found broad applications in gene discovery and gene expression profiling. Recently, a number of studi...
