Time-resolved and multi-tissue RNAseq provides new insights on the immune responses of European eels following infection with Aeromonas hydrophila

No studies have systematically compared time-resolved and multi-tissue innate immune responses for European eels ( Anguilla anguilla ) with Aeromonas hydrophila infection by a high throughput method. Here, we challenged European eels with A. hydrophila (infected) or PBS (control). A low fatality rate (16.1%) was observed for the infected group at 2 ​d post-infection (dpi). Then we examined transcriptional profiles of intestines, livers and spleens from 12 European eels with/without infection by A. hydrophila at 6, 18 and 36 ​h post-infection (hpi). The results showed that the most differentially expressed genes (DEGs) were found in the spleen at 6 hpi (7569 DEGs), followed by the intestine at 6 hpi (3129 DEGs) and the liver at 18 hpi (2722 DEGs). Only 540, 41 and 130 DEGs were found in the spleen, liver, and intestine at 36 hpi, respectively. The comparison of DEG numbers and enriched KEGG pathways suggested a consistent time-course immune response in these tissues. A similar enrichment of pattern recognition receptors-related pathways including Toll-like receptors, NOD-like receptors and RIG-I-like receptors was found in the liver and spleen, but not in the intestine. Among immune-related DEGs, 62 paralogue pairs were found, and the expression trends of most paralogues were consistent. Some paralogues of immune-related DEGs had unique domains. Furthermore, large clusters representing similar tissue were shown for the intestine and spleen. A different co-expression network involved in cytokine signal transduction and interaction existed between the liver and spleen. This study has provided time-resolved and multi-tissue transcriptome characteristics of A. anguilla in response to A. hydrophila infection. • Consistent time-course immune responses among spleens, livers and intestines. • A similar enrichment of TLRs, NLRs and RLRs was revealed in the livers and spleens. • The expression trends of most paralogues groups were consistent. • No common hub gene was found between the livers and spleens tissues. • The relationship between the intestines and spleens was much closer.