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In recent years, apple fruits of Malus pumila Mill cv.Fushi have been damaged by a dapple disease showing yellow spots on their surface induced by Apple scar skin viroid (ASSVd), and decreased their market value significantly by cutting down 2 to 3 folds than the normal fruits in price in China.Many ASSVd variant sequences have been reported, while whether there are some genomic motifs within the viroid sequence modulating their pathogenicity keeps unknown.