CLVd viroid amplicon sequencing

Columnea latent viroid (CLVd) is one of the most serious tomato diseases causing serious yield loss, fruit quality and affects international tomato seed trade. Having highest mutation rates in their replication process, viroids co-exist in their host as a population of variants, so-called quasispecies, showing a huge level of genetic diversity. To study the population of CLVd in individual host plants, we used amplicon sequencing using specific CLVd primers linked with an eight bases sample-tagging sequence, to amplify libraries. An infectious clone of a CLVd isolate (Chaipayon-1; KM214216) was inoculated on different solanaceaous host plants, namely tomato (cv. Insaf and Rutgers), bolo maka (Solanum stramoniifolium), Thai round eggplant (Solanum melongena), and pepper (Capsicum annuum).