Abstract: 【Aim】 Based on the previously gained miRNA and mRNA omics datasets, bioinformatic prediction, database annotation and regulatory network analysis of differentially expressed mRNAs (DEmRNAs) in the midgut of Apis mellifera ligustica workers targeted by differentially expressed miRNAs (DEmiRNAs) of Nosema ceranae were conducted in this study, aiming to uncover the regulation of gene expression in the midgut of A. m. ligustica by N. ceranae. 【Methods】 Significant DEmRNAs of A. m. ligustica workers were screened by comparison of miRNA data from the midgut of A. m. ligustica workers at 7 d (AmT1) and 10 d (AmT2) post N. ceranae infection and the corresponding uninfected midguts (AmCK1 and AmCK2, respectively), while significant DEmiRNAs of N. ceranae were screened through comparison of miRNA data from N. ceranae infecting the midgut of A. m. ligustica workers (NcT1 and NcT2, respectively) and clean fungal spores (NcCK). DEmRNAs in the midgut of A. m. ligustica workers targeted by N. ceranae DEmiRNAs were predicted using TargetFinder software. GO and KEGG database annotations of the aforementioned target DEmRNAs in the midgut of A. m. ligustica workers were performed with related bioinformatic tools. Following KEGG database annotations, DEmRNAs in the midgut of A. m. ligustica workers relative to immune defense and energy metabolism were filtered out, followed by construction and investigation of the regulatory networks between the abovementioned DEmRNAs in the midgut of A. m. ligustica workers and the corresponding N. ceranae DEmiRNAs. 【Results】 In the NcCK vs NcT1 comparison group, 77 significantly up-regulated miRNAs and 52 significantly down-regulated miRNAs of N. ceranae could respectively target 118 significantly down-regulated mRNAs and 135 significantly up-regulated mRNAs in the midgut of A. m. ligustica workers in the AmCK1 vs AmT1 comparison group, and these mRNAs could be annotated to 31 and 25 GO terms and 113 and 107 KEEG pathways, respectively. In the NcCK vs NcT2 comparison group, 52 significantly up-regulated miRNAs and 49 significantly down-regulated miRNAs of N. ceranae could respectively target 97 significantly down-regulated mRNAs and 210 significantly up-regulated mRNAs in the midgut of A. m. ligustica workers in the AmCK2 vs AmT2 comparison group, and these mRNAs could be annotated to 27 and 30 GO terms and 97 and 127 KEGG pathways, respectively. Moreover, 11 shared significantly up-regulated miRNAs and 19 shared significantly down-regulated miRNAs in the NcCK vs NcT1 and NcCK vs NcT2 comparison groups could respectively target six shared significantly down-regulated mRNAs and 14 shared significantly up-regulated mRNAs in the midgut of A. m. ligustica workers in the AmCK1 vs AmT1 and AmCK2 vs AmT2 comparison groups, which could be annotated to 7 and 10 GO terms and 0 and 9 KEEG pathways, respectively. DEmiRNAs in the NcCK vs NcT1 and NcCK vs NcT2 comparison groups could target DEmRNAs associated with energy metabolism pathways including oxidative phosphorylation and sulfur metabolism, and immune defense pathways such as endocytosis, melanogenesis, lysosome, autophagy, Toll-like receptor signaling pathway, apoptosis, Ras signaling pathway, ubiquitin-mediated proteolysis, and MAPK signaling pathway in the midgut of A. m. ligustica workers in the AmCK1 vs AmT1 and AmCK2 vs AmT2 comparison groups. Further analysis indicated that miR-216-x, miR-5119-y, bantam-y and miR-8-y were all significantly up-regulated in both the NcCK vs NcT1 and NcCK vs NcT2 comparison groups, and targeted several significantly down-regulated mRNAs relative to immune defense pathways such as lysosome, melanogenesis, ubiquitin-mediated proteolysis, MAPK signaling pathway and Ras signaling pathway in the midgut of A. m. ligustica workers. 【Conclusion】 DEmiRNAs of N. ceranae may exert extensive effects on gene expression in A. m. ligustica workers during the infection process. N. ceranae is likely to enhance its infection through cross-kingdom regulation of immune defense of A. m. ligustica workers via up-regulating some miRNAs, and increase energy stealing and proliferation by cross-kingdom regulation via down-regulating some miRNAs.

Key words: Nosema ceranae, Apis mellifera ligustica, microRNA, immune defense, energy metaboliam, gene expression regulation, midgut