Abstract: 【Aim】 The microsporidian Nosema bombycis can produce epizootic outbreaks in populations of the domestic silkworm (Bombyx mori) by the major mode of vertical transmission and horizontal transmission. In order to explore the genomic defense system against repetitive elements and potential means of gene regulation in N. bombycis, we conducted the survey of small RNAs associated with transposons and identification of the potential miRNAs in this silkworm parasite. 【Methods】 Total RNAs were extracted from silkworm midguts infected by N. bombycis spores and small RNA cDNA libraries were constructed for deep sequencing. After Solexa sequencing, we performed the functional characterization of N. bombycis small RNAs based on the reference genomic sequence through bioinformatics. 【Results】 N. bombycis has predominantly small RNAs with the length of 24 and 25 nt, most of which show a strong base bias for U at the 5′ end. Redundant small RNAs were associated with transposons in N. bombycis, and the amount of antisense small RNAs aligned with transposons was much more than that of sense small RNAs. Thirty-one candidate miRNAs were characterized by means of computational prediction, and certain miRNAs were shared by other Nosema species, suggesting that they may evolve conservatively. 【Conclusion】 There should exist small RNAs genomic defense system against transposons in N. bombycis. Tentative identification of potential thirtyone miRNAs provides a basis for further functional research of their targets.

Key words: Nosema bombycis, small RNAs, transposon, miRNA, genome