The early response expression profiles of miRNA-mRNA in farmed yellow catfish (Pelteobagrus fulvidraco) challenged with Edwardsiella tarda infection

Edwardsiella tarda , the bacterial pathogen that causes ascites disease and red-head disease, poses a serious threat to yellow catfish (Pelteobagrus fulvidraco) aquaculture. In this study, the spleens of E. tarda-infected and non infected yellow catfish were sequenced to obtain the microRNA (miRNA) and mRNA expression profiles. We obtained 657 differentially expressed (DE) miRNAs and 6867 DE mRNAs between two groups and annotated them using the KEGG database. In addition, the 43 negatively correlated miRNA-mRNA pairs were identified using integrated miRNA-mRNA analysis, which including immune-related miRNAs and target genes such as miR144, miR-1260, miR-1388, miR-33, miR-338, miR-181b, miR-34c, miR-135 and CLEC4E , LITR , PIKfyve , NCF4 , IL12? , IP6K2 , TNFRSF9 , IL-4R? , IRF2 , Mx2. We verified 8 DE miRNAs pairs and 10 DE mRNAs by quantitative realtime PCR. Finally, the CLEC4E and Mx2 mRNAs were selected for further verification using in situ hybridization. Together, our results provide valuable information for further analyses of the mechanisms of yellow catfish defense against E. tarda infection.

Automated summary

This study sequenced the spleens of E. tarda-infected and non-infected yellow catfish to obtain miRNA and mRNA expression profiles, identifying large numbers of differentially expressed miRNAs and mRNAs and annotating key genes. Through integrated miRNA-mRNA analysis, immune-related miRNA-mRNA pairs were identified, and some differentially expressed miRNAs and mRNAs were verified. Further verification of selected mRNAs using in situ hybridization provided valuable information for understanding the mechanisms of yellow catfish defense against E. tarda infection.