Viroid RNAs are targeted by Dicer-like enzymes and, as a consequence, viroidderived small RNAs (vd-sRNAs) with structural features similar to the small interfering RNAs (siRNAs) and microRNAs (miRNAs) accumulate in the infected tissues.Several studies have demonstrated that deep sequencing of small RNAs (sRNAs) from viroid-infected plants provides vd-sRNAs covering the entire genome,thus indicating that the source viroid can be in principle reconstructed.