Insights into the genetic diversity and evolution of L ittle cherry virus 1

• Published in: Plant pathology 2015-08, Vol.64 (4), p.817-824
• Main Authors: Katsiani, A. T., Maliogka, V. I., Amoutzias, G. D., Efthimiou, K. E., Katis, N. I.
• Format: Article
• Language: English
• ISSN: 0032-0862; 1365-3059
• DOI: 10.1111/ppa.12309

Little cherry virus 1 ( LC h V ‐1), a member of the recently proposed genus V elarivirus , is a sweet cherry pathogen that has been recently reported to infect other P runus species and is associated with various plant disorders. In this work the incidence of the virus on its putative hosts and possible mechanisms driving its evolution were investigated. Due to problems encountered with LC h V ‐1 detection, a new nested RT ‐ PCR assay was developed and applied. The virus was found to be prevalent in cherry plantations in G reece and only occasionally detected in other P runus species. Sequences corresponding to the partial RNA ‐dependent RNA polymerase ( R d R p ), heat‐shock protein homologue ( HSP 70h ) and coat protein ( CP ) genes were determined from G reek LC h V ‐1 isolates originating from different hosts; these were analysed, along with published homologous genomic regions from other isolates. Phylogenetic analysis of the three genes revealed the segregation of four evolutionary distinct groups showing no host or geography‐based clustering. Mean genetic distances among the four groups were high with the CP region showing the highest divergence, although intragroup variability levels were low. Nevertheless, estimations of the mean ratio of nonsynonymous substitutions per synonymous site to synonymous substitutions per synonymous site (d N /d S ) for the partial R d R p , HSP 70h and CP indicated that these genomic regions are under negative selection pressure. Interestingly, a recombination event was identified at the 3′ end of R d R p on a G reek virus isolate, thus highlighting the role of this mechanism in the evolutionary history of LC h V ‐1.