Identification of differentially expressed miRNAs through high-throughput sequencing in the chicken lung in response to Mycoplasma gallisepticum HS

Mycoplasma gallisepticum (MG) infects chickens, causes chronic respiratory diseases (CRD) and severely damages the poultry industry. It has been suggested that micro-ribonucleic acids (miRNAs) are involved in microbial pathogenesis. Here, we identified miRNAs that are associated with MG infection in chicken lungs at 3 and 10 days post-infection by deep sequencing. Thirty-six down-regulated and 9 up-regulated miRNAs belonging to 31 miRNA families were detected at 3 days post-infection, whereas 50 down-regulated and 18 up-regulated miRNAs belonging to 41 miRNA families were found at 10 days post-infection. The 45 and 68 differentially expressed miRNAs at 3 and 10 days target 6280 and 7181 genes, respectively. In this study, 8 candidate novel chicken miRNAs were identified. Analyses via GO, KEGG, miRNA-GO-network, path-net and gene-net showed that these altered miRNAs might be involved in regulating the host response to MG infection by targeting genes in many pathways, such as the MAPK pathway, focal adhesion, Wnt pathway, endocytosis, Jak/STAT pathway, phosphatidylinositol pathway, adherens junctions, regulation of actin cytoskeleton among others. These analyses indicate that the MAPK pathway may be a key regulatory route. Also, the miR-8 family, miR-499 family, miR-17 family, and PIK3 family genes, as well as the MAP2K1 and RAC1 genes, might be important in MG infection. miR-20 of the miR-17 family was further confirmed by RT-qPCR. The important miRNAs, mRNAs and pathways associated with MG infection in chicken are valuable for further research. Our data provide new insights into the mechanism of these miRNAs on the regulation of host-MG interactions.