Molecular Variability of Hop stunt viroid: Identification of a Unique Variant with a Tandem 15-nucleotide Repeat from Naturally Infected Plum Tree

Abstract

For this study, 68 plum samples were collected from 12 provinces of China. Low molecular weight RNAs were extracted and used for dot-blot, reverse transcription-polymerase chain reaction (RT-PCR), return-polyacrylamide gel electrophoresis, and biological indexing using cucumber. Results showed that 15 out of the 68 plum samples were positive for Hop stunt viroid (HSVd). Four positive samples were selected for cloning and sequence analysis. Results indicated that most HSVd sequences from the plum in China had 1-3 nucleotide changes from the closest HSVd in GenBank. In addition, the sample PB21 (cv. 'Friar') collected from Hebei province had one sequence with a 15-nt duplication (named HSVd D-15) at the 244/245 position in the lower central region. By biological indexing, cucumber seedlings, an indicator plant for HSVd, were inoculated with RNAs directly extracted from the original plum source (PB21, cv. 'Friar'). Nucleotide sequencing analysis of the progeny showed that HSVd, but not HSVd-D15, was recovered from inoculated cucumbers. Although very unlikely, the possibility that this extra sequence was the result of a PCR artifact cannot be completely ruled out.