Genetic diversity among endogenous plant pararetroviral sequences from geographically diverse sources of dahlia (Dahlia spp).
Druffel, K. L.
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Two distinct caulimoviruses, Dahlia mosaic virus (DMV) and Dahlia common mosaic virus (DCMV), and an endogenous plant pararetroviral sequence (DvEPRS) were reported in Dahlia spp. DvEPRS, previously referred to as DMV-D10, was originally isolated in the US from the cultivated Dahlia variabilis, and has been also found in New Zealand, Lithuania and Egypt as well as in wild dahlia species growing in their natural habitats in Mexico. Here we report the complete genome sequences of three new DvEPRS isolates from a Lithuanian cultivar (7159 nt), a New Zealander cultivar (7156 nt) and from the wild dahlia species, D. rupicola (7133 nt). The three have the structure and organization typical of a caulimovirus species and showed identities between 71 and 97% at the nucleotide level (nt) among various open reading frames (ORFs) when compared to those of DvEPRS. To better understand the genetic diversity, DvEPRS from cultivated and wild dahlia species were compared. A total of 7 full-length sequences were used for phylogenetic analyses, mutation frequencies, potential recombination events, selection and fitness as evolutionary evidences for genetic diversity. Phylogentic analyses showed one clade of all DvEPRS indicating a lack of clustering by geographical origin. When the various DvEPRS were grouped into two taxa, no difference was observed between those from cultivated and wild dahlia species. Assessment of population genetic parameters found strong negative selection for all ORFs, with the replicase region more variable than other ORFs. Identification of potential recombination events involving parents from different lineages provided strong evolutionary evidence for genetic diversity among various DvEPRS. This study contributes to an increased understanding of molecular population genetics and evolutionary pathways of these reverse transcribing viral elements.