Analysis of the transcriptomic profilings of Mandarin fish (Siniperca chuatsi) infected with Flavobacterium columnare with an emphasis on immune responses

• The transcriptomic profiles of the head kidneys from Flavobacterium columnare (FC) infected and non-infected Mandarin fish.
• Totally 31,168 unigenes with high quality were obtained.
• Totally 1019 genes expressed differently in the FC-infected and non-infected groups were identified, including 603 up-regulated genes and 416 down-regulated genes.
• 27 immune related genes which were differently expressed in the FC-infected and non-infected groups were scrutinized. Six of differently expressed genes were chosen for further validation using qRT-PCR.

Flavobacterium columnare (FC) is the causative pathogen of columnaris which has caused great economic loss in fish culture worldwide, including in Mandarin fish (Siniperca chuatsi) culture. In the present study, the transcriptomic profiles of the head kidneys from FC-infected and non-infected Mandarin fish were obtained using HiSeq™ 2000 (Illumina). Totally 31,168 unigenes with high quality were obtained. Genes involved in protein folding, metabolism and energy, immune responses, oxidoreductase activity, cell growth and death were identified as enriched classes. 1019 differently expressed genes between the two groups were identified, including 603 up-regulated and 416 down-regulated genes. 27 differently expressed immune related genes were scrutinized, including 17 up-regulated and 10 down-regulated genes. Six of the differently expressed genes were further validated by qRT-PCR. The roles of the immune related genes were discussed. Identification of the host genes in response to FC infection will shed a new light on the prevention of columnaris.