| Summary: | The microsporidium <i>Nosema ceranae</i> is a high prevalent parasite of the European honey bee (<i>Apis mellifera</i>). This parasite is spreading across the world into its novel host. The developmental process, and some mechanisms of <i>N. ceranae</i>-infected honey bees, has been studied thoroughly; however, few studies have been carried out in the mechanism of gene expression in <i>N. ceranae</i> during the infection process. We therefore performed the suppressive subtractive hybridization (SSH) approach to investigate the candidate genes of <i>N. ceranae</i> during its infection process. All 96 clones of infected (forward) and non-infected (reverse) library were dipped onto the membrane for hybridization. A total of 112 differentially expressed sequence tags (ESTs) had been sequenced. For the host responses, 20% of ESTs (13 ESTs, 10 genes, and 1 non-coding RNA) from the forward library and 93.6% of ESTs (44 ESTs, 28 genes) from the reverse library were identified as differentially expressed genes (DEGs) of the hosts. A high percentage of DEGs involved in catalytic activity and metabolic processes revealed that the host gene expression change after <i>N. ceranae</i> infection might lead to an unbalance of physiological mechanism. Among the ESTs from the forward library, 75.4% ESTs (49 ESTs belonged to 24 genes) were identified as <i>N. ceranae</i> genes. Out of 24 <i>N. ceranae</i> genes, nine DEGs were subject to real-time quantitative reverse transcription PCR (real-time qRT-PCR) for validation. The results indicated that these genes were highly expressed during <i>N. ceranae</i> infection. Among nine <i>N. ceranae</i> genes, one <i>N. ceranae</i> gene (AAJ76_1600052943) showed the highest expression level after infection. These identified differentially expressed genes from this SSH could provide information about the pathological effects of <i>N. ceranae</i>. Validation of nine up-regulated <i>N. ceranae</i> genes reveal high potential for the detection of early nosemosis in the field and provide insight for further applications.
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