Identification in eggplant of a variant of citrus exocortis viroid (CEVd) with a 96 nucleotide duplication in the right terminal region of the rod-like secondary structure

Analysis of eggplants, kept for years under greenhouse conditions after having been mechanically inoculated with nucleic acid preparations from field-grown eggplants containing two viroids, Eggplant latent viroid (ELVd) and Citrus exocortis viroid (CEVd), revealed the presence of an additional larger viroid RNA. Molecular characterization of this RNA showed that it is a stable 467-nt variant of CEVd with a 96-nt duplication of the right terminal region (CEVd-D96) that preserves the rod-like secondary structure. The coexistence in eggplant of CEVd (371 nt) and CEVd-D96, and the fact that they have an almost identical sequence, strongly suggests the emergence of the latter from the former through an internal recombination mediated by a jumping RNA polymerase with low processivity. CEVd-D96 from eggplant is similar to the CEVd-D92 variant characterized previously in a hybrid tomato, suggesting that certain hosts may play a critical role in selecting and replicating this class of enlarged variants.