Abstract
Ectoparasitic dinoflagellate Amyloodinium ocellatum (AO) is one of the most pathogenic protozoan parasites, causing amyloodiniosis in temperate and tropical marine fish. Golden pompano is susceptible to AO and increasing outbreaks of AO have posed a major threat to the economic sustainability of intensive aquaculture industry. In this study, natural parasite infection was simulated, and whole transcriptome analysis was performed with infected golden pompano gills to explore the host immune response to AO infestation. Overall, 4388 differentially expressed (DE) genes, 395 DE long non-coding RNAs (lncRNAs), 10 DE circular RNAs (circRNAs) and 96 DE microRNAs (miRNAs) were identified. DE genes were involved in pathways of ECM-receptor interaction and cytokine-cytokine receptor interaction, including many crucial extracellular matrix (ECM) components (integrin, laminin and collagen), cytokines (interleukin and lymphotoxin) and C-C motif chemokines. DE lncRNAs were significantly enriched in the regulation of immune cells, such as monocytes, neutrophils and lymphocytes. DE circRNAs were notably correlated with NOD-like receptor signaling pathway. DE miRNAs were prominently associated with immune-related pathways of cytokine-cytokine receptor interaction, intestinal immune network for IgA production, herpes simplex infection and TGF-beta signaling pathway. Furthermore, a core competing endogenous RNA (ceRNA) network was constructed, consisting of 28 DE mRNAs, 21 DE miRNAs, 8 DE circRNAs and 58 DE lncRNAs. The key roles of cytokine-cytokine receptor interaction, focal adhesion, MAPK signaling, NOD-like receptor signaling and mTOR signaling pathway were highlighted in the ceRNA network. In total, the present study uncovered the molecular changes of coding and non-coding RNAs involved in host immune response induced by AO infestation. The results could contribute significantly to a comprehensive understanding of host immune response to AO infestation and provide new clues for developing efficient amyloodiniosis control measures and germplasm improvement in artificial breeding of golden pompano.
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