Sequence variability ofChrysanthemum stunt viroidin different chrysanthemum cultivars.
Viroids are the smallest infectious agents, and their genomes consist of a short single strand of RNA that does not encode any protein.Chrysanthemum stunt viroid(CSVd), a member of the familyPospiviroidae, causes chrysanthemum stunt disease. Here, we report the genomic variations of CSVd to understand the sequence variability of CSVd in different chrysanthemum cultivars. We randomly sampled 36 different chrysanthemum cultivars and examined the infection of CSVd in each cultivar by reverse transcription polymerase chain reaction (RT-PCR). Eleven cultivars were infected by CSVd. Cloning followed by Sanger sequencing successfully identified a total of 271 CSVd genomes derived from 12 plants from 11 cultivars. They were further classified into 105 CSVd variants. Each single chrysanthemum plant had a different set of CSVd variants. Moreover, different single plants from the same cultivar had different sets of CSVd variants but identical consensus genome sequences. A phylogenetic tree using 12 consensus genome sequences revealed three groups of CSVd genomes, while six different groups were defined by the phylogenetic analysis using 105 variants. Based on the consensus CSVd genome, by combining all variant sequences, we identified 99 single-nucleotide variations (SNVs) as well as three nucleotide positions showing high mutation rates. Although 99 SNVs were identified, most CSVd genomes in this study were derived from variant 1, which is identical to known CSVd SK1 showing pathogenicity.
Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea.
Hoseong
H
Choi
Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea.
Yeonhwa
Y
Jo
Virology Unit, Department of Horticultural Environment, National Institute of Horticultural and Herbal Science, RDA, Wan-Ju, Republic of Korea.
Ju-Yeon
JY
Yoon
Virology Unit, Department of Horticultural Environment, National Institute of Horticultural and Herbal Science, RDA, Wan-Ju, Republic of Korea.
Seung-Kook
SK
Choi
Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea.
Won Kyong
WK
Cho
Chrysanthemum; Chrysanthemum stunt viroid; Cultivar; Sequence variability