Comprehensive analysis of genomic variation of Hop stunt viroid

Hop stunt viroid (HSVd) infects a wide range of plants. In this study, we assembled de novo two HSVd genomes from the transcriptome of an apricot species. To examine HSVd variation in a single tree, we sequenced 70 HSVd genomes from unique apricot and plum trees and identified 11 HSVd variants. In addition, we analysed all known 572 HSVd sequences and identified 382 non-redundant HSVd variants. Phylogenetic analysis identified five groups of the 382 HSVd variants. Furthermore, we generated a consensus HSVd sequence by averaging across all 382 sequences. Comparative sequence analysis identified several regions showing sequence variation, while the terminal left region of the rod-like structure was highly conserved.