Molecular characterization of Plum pox virus Rec isolates from Russia suggests a new insight into evolution of the strain
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Field isolates of Plum pox virus (PPV), belonging to the strain Rec, have been found for the first time in Russia. Full-size genomes of the isolates K28 and Kisl-1pl from myrobalan and plum, respectively, were sequenced on the 454 platform. Analysis of all known PPV-Rec complete genomes using the Recombination Detection Program (RDP4) revealed yet another recombination event in the 5′-terminal region. This event was detected by seven algorithms, implemented in the RDP4, with statistically significant P values and supported by a phylogenetic analysis with the bootstrap value of 87%. A putative PPV-M-derived segment, encompassing the C-terminus of the P1 gene and approximately two-thirds of the HcPro gene, is bordered by breakpoints at positions 760–940 and 1838–1964, depending on the recombinant isolate. The predicted 5′-distal breakpoint for the isolate Valjevka is located at position 2804. The Dideron (strain D) and SK68 (strain M) isolates were inferred as major and minor parents, respectively. Finding of another recombination event suggests more complex evolutionary history of PPV-Rec than previously assumed. Perhaps the first recombination event led to the formation of a PPV-D variant harboring the PPV-M-derived fragment within the 5′-proximal part of the genome. Subsequent recombination of its descendant with PPV-M in the 3′-proximal genomic region resulted in the emergence of the evolutionary successful strain Rec.
KeywordsPlum pox virus Strain Rec 454 pyrosequencing Phylogenetic analysis Recombination analysis Evolution
This study was funded by the Russian Science Foundation (Grant No 14-24-00007). The next generation sequencing on 454 platform was supported by the Russian Foundation for Basic Research (Grant No 14-04-01786).
SC, IM, and AK designed the experiments; AS, AK, and PI performed the experiments; SC, PI, IM, AK, and AS analyzed the data; SC, PI, and IM wrote the paper.
Compliance with ethical standards
Conflict of interest
The authors declare no conflict of interests.
This article does not contain any studies with human participants or animals performed by any of the authors.
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