Integrated analysis of miRNAome and transcriptome reveals miRNA-mRNA network regulation in Vibrio alginolyticus infected thick shell mussel Mytilus coruscus

The thick shell mussel Mytilus coruscus has developed into a model species for studying the interaction between molluscs and environmental stimuli. Herein, integrated analysis of miRNAome and transcriptome was performed to reveal miRNA-mRNA network regulation in Vibrio alginolyticus infected M. coruscus. There have detected some histological abnormalities in digestive gland and gills of V. alginolyticus challenged mussels, ascertaining the effective irritation by the present bacterial strain. A total of 265 novel miRNAs were finally predicted, of which 26 were differentially expressed miRNAs (DEMs). Additionally, 667 differentially expressed genes (DEGs) were detected, which may be potentially associated with innate immune response to V. alginolyticus infection. A regulatory network linked to 22 important pathways and 16 DEMs and 34 OGs was constructed. Some traditional immune-related signaling pathways such as toll-like receptor signaling pathway (TLR) signaling pathway, transforming growth factor-beta (TGF-beta) signaling pathway, peroxisome, phagosome, lysosome, mammalian target of rapamyoin (mTOR) signaling pathway were linked to specific miRNAs and genes in this network. Further, interactional relationship between certain miRNAs and TLR pathway was dissected, which the results predicted that a number of TLRs and TLR-associated signaling genes including TLR1, TLR2, TLR4, TLR6, IRAK1, TRAF6, MAPK, and IL-17 were negatively regulated by novel_miR_11, novel_miR_145, novel_miR_196, novel_miR_5, novel_miR_163 and novel_miR_217 in the TLR pathway. Additionally, interactional relationship between novel_miR_145 and TLR2 was validated by laboratory experiment. The integrated analysis of mRNA and microRNA deep sequencing data exhibited a sophisticated miRNA-mRNA regulation network in M. coruscus in response to V. alginolyticus challenge, which shed a new light on the underlying mechanism of molluscan confronting bacterial infection.

Automated summary

The study revealed a sophisticated miRNA-mRNA regulation network in M. coruscus in response to V. alginolyticus challenge, linking immune-related signaling pathways with specific miRNAs and genes. It also dissected the interactional relationship between certain miRNAs and the TLR pathway, predicting negative regulation of TLRs and associated genes by novel miRNAs. Additionally, a laboratory experiment validated the interactional relationship between novel miR-145 and TLR2.