Transcriptome profiling of grass carp (Ctenopharyngodon idellus) infected with Aeromonas hydrophila

•Transcriptome analysis of the grass carp infected Aeromonas hydrophila was performed.•2121 differential expression genes were identified.•105 important immune related genes were categorized and discussed.•For a better understanding of immune mechanism of grass carp infected bacteria.

Aeromonas hydrophila is the causative pathogen of intestinal hemorrhage which has caused great economic loss in grass carp aquaculture. In order to understand the immunological response of grass carp to infection by A. hydrophila, the transcriptomic profiles of the spleens from infected and non-infected grass carp groups were obtained using HiSeq™ 2500 (Illumina). An average of 63 million clean reads per library was obtained, and approximately 80% of these genes were successfully mapped to the reference genome. A total of 1591 up-regulated and 530 down-regulated genes were identified. Eight immune-related categories involving 105 differently expressed genes were scrutinized. 16 of the differently expressed genes involving immune response were further validated by qRT-PCR. Our results provide valuable information for further analysis of the mechanisms of grass carp defense against A. hydrophila invasion.