Sequence Analysis of Potato Spindle Tuber Viroid Isolates in Yunnan

Purpose Our aim was to understand the molecular variation and pathogenic mechanism of potato spindle tuber viroid (PSTVd) of Yunnan Province.Method The suspected tubers of PSTVd were collected from two different areas in Yunnan. Total RNA was extracted and reverse transcripted to cDNA. RT-PCR detection was conducted using PSTVd specific primers, and then the amplified products were purified, cloned and sequenced.ResultsThe results showed that the full length fragments of PSTVd are 357 bp, which named as PSTVd-DasongpingYN (KX159281) and PSTVd-LiangheYN (KX159282), respectively. The phylogenetic trees were constructed with two PSTVd isolates from Yunnan and other PSTVd strains reported worldwide. Meanwhile, the sequence comparison and the second structure prediction were analyzed among PSTVd-DasongpingYN, PSTVd-LiangheYN and different pathogenic PSTVd strains (mild, medium and severe), indicating that the PSTVd-DasongpingYN and PSTVd-LiangheYN were more close to the mild PSTVd strains.ConclusionThe similarity of PSTVd-DasongpingYN and PSTVd-LiangheYN was 97.5%. There are 9 different bases mainly concentrated in the variable region (V) and the right terminal region (TR) which implied that there are obvious differences in two PSTVd Yunnan isolates. PSTVd-DasongpingYN and PSTVd-LiangheYN belong to the mild strain of PSTVd.