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Two sugarcane varieties,Yacheng 05-179 (smut resistant) and ROC 22 (smut susceptible),were used as the plant materials.Sugarcane buds challenged by S.scitamineum at 48 hours after inoculation (hpi) were taken as treatment group and those treated by water as the control group.We used high-throughput HiSeq sequencing technology to analyze the differentially expressed microRNAs in sugarcane challenged by S.scitamineum at 48 hpi,then small RNA sequences were annotated and the differentially expressed miRNAs were screened.