Identification of Differential Expression microRNAs and Target Genes Analysis of Sea Cucumber (Apostichopus japonicus) in Response to Vibrio splendidus Infection

Abstract

microRNAs (miRNAs), involved in post-transcriptional gene regulation, play important roles in the growth, development, cell differentiation, and immune defense of eukaryotes. Apostichopus japonicus has become an economically important species for marine aquaculture in China; however, the outbreak of diseases, such as skin ulcer syndrome (SUS), has led to great losses in aquaculture development. Therefore, molecular mechanisms underlying disease occurrence must be further elucidated. In the present study, Vibrio splendidus, an important causative pathogen of SUS, was used as the stress strain (1×106 CFU/mL) in an artificial infection experiment. Body wall of the diseased (PT16S) and healthy (PT10H) samples was subjected to miRNA-Seq. Differentially expressed miRNAs (DEmiRNAs) were screened using bioinformatics. The target genes of DEmiRNAs were predicted and used for constructing miRNA-mRNA regulatory networks. Through miRNA-Seq, respectively 5 902 588 and 5 053 529 valid reads were generated for the PT10H and PT16S samples. A total of 13 DEmiRNAs (P≤0.05) were screened between PT10H and PT16S, of which two were upregulated and 11 downregulated. Target gene prediction revealed that the two upregulated DEmiRNAs bound to 3010 target genes, which were annotated to 585 GO terms and 24 signaling pathways (P≤0.05), while the 11 downregulated DEmiRNAs bound to 19 072 target genes, which were annotated to 514 GO terms and 22 signaling pathways (P≤0.05). In the validation test, the consistency rate of the sequencing and qRT-PCR data reached 70%. Two immune-related pathways (ubiquitin-mediated proteolysis and Notch signaling) were selected and used to construct the miRNA-mRNA regulatory networks. The 13 DEmiRNAs could bind 134 ubiquitin-mediated proteolytic mRNAs and 109 Notch signaling mRNAs. Specifically, Aja-miR-1559-3p, Aja-miR-7550-5p, Aja-miR-2478, and Aja-miR-9277-3p may be involved in the regulation of ubiquitin-mediated proteolysis and Notch signaling. Our results provide primary data for understanding the post-transcriptional regulatory mechanisms of diseases in sea cucumber.

Keywords

• apostichopus japonicus
• microrna
• vibrio splendidus
• stress response
• target genes
• mirna-mrna network