Sequence variability of Chrysanthemum stunt viroid in different chrysanthemum cultivars

PeerJ

article

Hoseong Choi¹  Yeonhwa Jo¹  Ju-Yeon Yoon²  Seung-Kook Choi²  Won Kyong Cho¹ 

[1] Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University;Virology Unit, Department of Horticultural Environment, National Institute of Horticultural and Herbal Science

关键词: Chrysanthemum stunt viroid;    Sequence variability;    Cultivar;    Chrysanthemum;   

DOI  :  10.7717/peerj.2933

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

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 family Pospiviroidae, 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.

【 授权许可】

CC BY