Phylogenetic analysis and molecular characterization of chrysanthemum chlorotic mottle viroid and chrysanthemum stunt viroid from chrysanthemum in Thailand

Abstract

Chrysanthemum chlorotic mottle viroid (CChMVd) and chrysanthemum stunt viroid (CSVd) are limiting factors for chrysanthemum cultivation and cause economic losses throughout the world. Chrysanthemum leaves were collected from Chiang Mai and Chiang Rai provinces of Thailand during 2019–2021. Both viroids were detected by using reverse transcription polymerase chain reaction (RT-PCR) and molecularly characterized. Six CChMVd and five CSVd amplicons were detected, cloned and sequenced. BLAST analysis revealed that CChMVd shared 93%–99% identical and CSVd shared 95%–99% identical with the representative species retrieved from GenBank, Moreover, the nucleotides at the position 82–85 of the tetraloop region were keys for CChMVd clusters resulting to the distinct clade of either symptomatic or non-symptomatic strains. The phylogenetic analysis of individual viroid represented that six CChMVd variants were closely related to Korea and China variants and clustered in the symptomatic clade of the Asia cluster. For CSVd, five variants in the present study were grouped with CSVd from Dahlia spp. of Japan. Predicted secondary structure of both viroids showed the distribution of sequence variations. The predicted secondary structure showed sequence variants of CChMVd were distributed on most of the secondary structure, whereas sequence variants of CSVd were frequently found in pathogenic, variable and terminal right domains. This study provides phylogenetic relationship of CChMVd and CSVd Thai variants along with their sequence variability.