Molecular characterization and phylogenetic analysis of Citrus viroid VI variants from citrus in China

Citrus viroid VI (CVd-VI) is a viroid originally found from citrus and persimmon in Japan. We report here the identification and molecular characterization of CVd-VI from four growth regions of China. A total of 90 cDNA clones from nine citrus cultivars were sequenced. The sequence homologies of the Chinese CVd-VI and the reference sequence (NC_004359) vary from 94.2% to 97%. The sequence homologies among the Chinese isolates were up to 95.2%. Phylogenetic analysis of the 23 CVd-VI variants from China and Japan showed that they were grouped into two clades, one with 20 citrus variants and another with three persimmon variants, regardless of the geographic origins. Therefore, as with Hop stunt viroid, CVd-VI could also be divided into two types, citrus and persimmon types. Sequence alignment showed that most nucleotide changes between the two clades occurred in the P, V and TL domains, and analysis indicated that these mutations influenced the predicted secondary structures under minimum energy.