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Molecular characterization of Plum pox virus Rec isolates from Russia suggests a new insight into evolution of the strain

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Abstract

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.

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Acknowledgements

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).

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Authors and Affiliations

  1. Lomonosov Moscow State University, Moscow, 119234, Russia

    Sergei Chirkov, Peter Ivanov & Anna Sheveleva

  2. Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia

    Anna Kudryavtseva

  3. Nikita Botanical Gardens - National Scientific Center, Yalta, 298648, Russia

    Irina Mitrofanova

Authors
  1. Sergei Chirkov
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  2. Peter Ivanov
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  3. Anna Sheveleva
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  4. Anna Kudryavtseva
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  5. Irina Mitrofanova
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Contributions

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.

Corresponding author

Correspondence to Sergei Chirkov.

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The authors declare no conflict of interests.

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This article does not contain any studies with human participants or animals performed by any of the authors.

Additional information

Edited by Seung-Kook Choi.

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11262_2018_1541_MOESM1_ESM.tif

Fig. S1 Agarose gel electrophoresis analysis of reverse-transcription polymerase chain reaction amplification products from PPV-infected leaf samples using PPV-Rec (mD5/mM3) and PPV-M (P1/PM) strain-specific primers. M - GeneRuler 100 bp DNA ladder (Thermo Scientific). The arrows on the right show the products specific for PPV-Rec (605 bp) and PPV-M (198 bp). Supplementary material 1 (TIFF 243 kb)

11262_2018_1541_MOESM2_ESM.pdf

Fig. S2 BootScan analysis of recombination in the 5′-proximal region of PPV-Rec genomes using the RDP4 package. Only 5′-proximal part of the genomes is shown. The names of isolates are presented above the pictures. Purple and sea-green lines indicate grouping of different parts of the PPV-Rec genomes with PPV-M (isolate SK-68) or PPV-D (isolate Dideron), respectively. Window 800 nt, step 20 nt. The dotted line shows an arbitrary 80% cut-off bootstrap support. Recombination region predicted by the RDP4 analysis is presented in pink. Numerals on the top of the pink area indicate average P-values. Supplementary material 2 (PDF 61 kb)

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Chirkov, S., Ivanov, P., Sheveleva, A. et al. Molecular characterization of Plum pox virus Rec isolates from Russia suggests a new insight into evolution of the strain. Virus Genes 54, 328–332 (2018). https://doi.org/10.1007/s11262-018-1541-8

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  • DOI: https://doi.org/10.1007/s11262-018-1541-8

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