Insight into Host-driven in Planta Evolution of Columnea Latent Viroid through Quasi-species Population

Abstract

With a high mutation rate and fast replication, a population of mutated viroid progenies is generated and co-exists in the same host plant as a population of variants (so-called quasi-species), showing a huge level of genetic diversity. In our work, we report the evidence of the quasi-species in CLVd in several solanaceous plants; tomato (Rutgers and Seda 50), bolo maka and eggplant. An infectious dsDNA CLVd was synthesized from the recombinant plasmid containing the full-length genome of CLVd isolate Solanum-1 (JF742632) and then inoculated on the plants under specific conditions. The initial inoculation only successfully infected tomato cv. Rutgers. This CLVd-infected Rutgers was used for subsequent inoculation of the above-mentioned host plants. When all host plants proved to be systemically infected, RNA extraction and RT-PCR were performed. To study the CLVd population in individual host plants, the specific CLVd primers linked with an eight base sample-tagging sequence were used for amplifying libraries. The average 20,237 CLVd reads per PCR-replicate and 22 progeny variants in total from the first infected tomato plant were obtained. Among these 22 of CLVd variants, we found 22 total number of single-nucleotide polymorphisms in which average three point-mutations per CLVd genome mainly in Terminal Right and Pathogenic domains were observed. In addition, the estimated mutation rate of CLVd was calculated at 8.15 X10-3. Our data demonstrate that CLVd in a host plant exists as a population of quasi-species while showing host specificity of the dominant variants as host-driven in planta evolution.