Virus Genes

, Volume 54, Issue 2, pp 328–332 | Cite as

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

  • Sergei Chirkov
  • Peter Ivanov
  • Anna Sheveleva
  • Anna Kudryavtseva
  • Irina Mitrofanova


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.


Plum 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).

Authors’ 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.

Compliance with ethical standards

Conflict of interest

The authors declare no conflict of interests.

Ethical approval

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

Supplementary material

11262_2018_1541_MOESM1_ESM.tif (244 kb)
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 (61 kb)
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)


  1. 1.
    M. Barba, A. Hadidi, T. Candresse, M. Cambra, in Virus and Virus-Like Diseases of Pome and Stone Fruits, ed. by A. Hadidi, M. Barba, T. Candresse, W. Jelkmann (APS Press, St. Paul, 2011), p. 185Google Scholar
  2. 2.
    Z. Subr, M. Glasa, Acta Virol. 57, 217 (2013)CrossRefPubMedGoogle Scholar
  3. 3.
    J.A. Garcia, M. Glasa, M. Cambra, T. Candresse, Mol. Plant. Pathol. 15, 226 (2014)CrossRefPubMedGoogle Scholar
  4. 4.
    M. Glasa, L. Palkovics, P. Kominek, G. Labonne, S. Pittnerova, O. Kudela, T. Candresse, Z. Šubr, J. Gen. Virol. 85, 2671 (2004)CrossRefPubMedGoogle Scholar
  5. 5.
    M. Glasa, T. Candresse, Virus Res. 108, 199 (2005)CrossRefPubMedGoogle Scholar
  6. 6.
    C. Ulubas Serçe, T. Candresse, L. Svanella-Dumas, L. Krizbai, M. Gazel, K. Cağlayan, Virus Res. 142, 121 (2009)CrossRefGoogle Scholar
  7. 7.
    D. James, D. Sanderson, A. Varga, A. Sheveleva, S. Chirkov, Phytopathology 106, 407 (2016)CrossRefPubMedGoogle Scholar
  8. 8.
    M. Glasa, T. Malinowski, L. Predajna, N. Pupola, D. Dekena, L. Michalczuk, T. Candresse, Phytopathology 101, 980 (2011)CrossRefPubMedGoogle Scholar
  9. 9.
    D. James, A. Varga, Virus Res. 110, 143 (2005)CrossRefPubMedGoogle Scholar
  10. 10.
    D. James, A. Varga, D. Sanderson, Can. J. Plant Pathol. 35, 431 (2013)CrossRefGoogle Scholar
  11. 11.
    M. Glasa, V. Marie-Jeanne, G. Labonne, Z. Šubr, O. Kudela, J.-B. Quiot, Eur. J. Plant Pathol. 108, 843 (2002)CrossRefGoogle Scholar
  12. 12.
    S. Gadiou, D. Safarova, M. Navratil, Eur. J. Plant Pathol. 121, 513 (2008)CrossRefGoogle Scholar
  13. 13.
    I. Kamenova, J. Plant Pathol. 96, 411 (2014)Google Scholar
  14. 14.
    P. Salamon, L. Palkovics, Eur. J. Plant Pathol. 108, 903 (2002)CrossRefGoogle Scholar
  15. 15.
    M.T. Cervera, J.L. Reichmann, M.T. Martin, J.A. Garcia, J. Gen. Virol. 74, 329 (1993)CrossRefPubMedGoogle Scholar
  16. 16.
    M. Glasa, S. Paunovic, D. Jevremovic, A. Myrta, S. Pittnerova, T. Candresse, Arch. Virol. 150, 2051 (2005)CrossRefPubMedGoogle Scholar
  17. 17.
    D. Jevremovic, S. Paunovic, Pestic. Phytomed. 29, 97 (2014)CrossRefGoogle Scholar
  18. 18.
    V. Kajic, S. Cerni, M. Krajacic, I. Mikec, D. Škoric, J. Plant Pathol. 90(S1), 9 (2008)Google Scholar
  19. 19.
    S. Matic, M. Al Rwahnih, A. Myrta, Plant. Pathol. 55, 11 (2006)CrossRefGoogle Scholar
  20. 20.
    A. Myrta, M. Al Rwahnih, V. Savino, J. Plant Pathol. 87, 127 (2005)Google Scholar
  21. 21.
    L. Svanella-Dumas, I. Maurice, V. Blin, R. Quaren, C. Birgaentzle, T. Candresse, Plant Dis. 99, 421 (2015)CrossRefGoogle Scholar
  22. 22.
    E. Kollerova, S. Novakova, Z. Šubr, M. Glasa, Plant Dis. 90, 1108 (2006)CrossRefGoogle Scholar
  23. 23.
    T. Candresse, L. Svanella-Dumas, P. Gentit, K. Caglayan, B. Cevik, Plant Dis. 91, 331 (2007)CrossRefGoogle Scholar
  24. 24.
    K. Gurkan, A. Ceylan, Turk. J. Agric. For. 40, 746 (2016)CrossRefGoogle Scholar
  25. 25.
    D. Thompson, A. Varga, H. De Costa, C. Birch, M. Glasa, D. James, Plant Dis. 93, 674 (2009)CrossRefGoogle Scholar
  26. 26.
    D.P. Martin, B. Murrell, M. Golden, A. Khoosal, B. Muhire, Virus Evol. 1, 1 (2015)CrossRefGoogle Scholar
  27. 27.
    T. Wetzel, T. Candresse, G. Macquaire, M. Ravelonandro, J. Dunez, J. Virol. Method 39, 27 (1992)CrossRefGoogle Scholar
  28. 28.
    T. Wetzel, T. Candresse, M. Ravelonandro, J. Dunez, J. Virol. Method 33, 355 (1991)CrossRefGoogle Scholar
  29. 29.
    M. Glasa, Y. Prikhodko, L. Predajna, A. Nagyova, Y. Shneyder, T. Zhivaeva, Z. Šubr, M. Cambra, T. Candresse, Phytopathology 103, 972 (2013)CrossRefPubMedGoogle Scholar
  30. 30.
    D. James, A. Varga, Acta Hortic. 657, 177 (2004)CrossRefGoogle Scholar
  31. 31.
    L. Nemchinov, A. Hadidi, J. Virol. Method 70, 231 (1998)CrossRefGoogle Scholar
  32. 32.
    A. Olmos, M. Cambra, M.A. Dasi, T. Candresse, O. Esteban, M.T. Gorris, M. Asensio, J. Virol. Method 68, 127 (1997)CrossRefGoogle Scholar
  33. 33.
    Z. Šubr, S. Pittnerova, M. Glasa, Acta Virol. 48, 173 (2004)PubMedGoogle Scholar
  34. 34.
    A. Sheveleva, A. Kudryavtseva, A. Speranskaya, M. Belenikin, N. Melnikova, S. Chirkov, Virus Genes 47, 385 (2013)CrossRefPubMedGoogle Scholar
  35. 35.
    T.A. Hall, Nucleic Acids Symp. Ser. 41, 95 (1999)Google Scholar
  36. 36.
    K. Tamura, J. Dudley, M. Nei, S. Kumar, Mol. Biol. Evol. 24, 1596 (2007)CrossRefPubMedGoogle Scholar
  37. 37.
    E.R. Chare, E.S. Holmes, Arch. Virol. 151, 933 (2006)CrossRefPubMedGoogle Scholar
  38. 38.
    M. Salminen, D. Martin, in The Phylogenetic Handbook: A Practical Approach to Phylogenetic Analysis and Hypothesis Testing, ed. by P. Lemey, M. Salemi, A.-M. Vandamme (Cambridge University Press, Cambridge, 2009), p. 519CrossRefGoogle Scholar
  39. 39.
    D. Sanderson, J. Fu, D. James, Acta Hortic. 1163, 107 (2017)CrossRefGoogle Scholar
  40. 40.
    I. Kamenova, J. Plant Pathol. 90(S1), 15 (2008)Google Scholar
  41. 41.
    I. Kamenova, E. Tasheva-Terzieva, K. Dragoyski, B. Stefanova, J. Phytopathol. 165, 602 (2017)CrossRefGoogle Scholar
  42. 42.
    I. Mikec, V. Kajić, M. Krajačić, D. Śkorić, Acta Hortic. 781, 193 (2008)CrossRefGoogle Scholar
  43. 43.
    L. Zagrai, I. Zagrai, B. Ferencz, I. Gaboreanu, K. Kovacs, I. Petricele, O. Popescu, D. Pamfil, N. Capote, J. Plant Pathol. 90(S1), 41 (2008)Google Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  • Sergei Chirkov
    • 1
  • Peter Ivanov
    • 1
  • Anna Sheveleva
    • 1
  • Anna Kudryavtseva
    • 2
  • Irina Mitrofanova
    • 3
  1. 1.Lomonosov Moscow State UniversityMoscowRussia
  2. 2.Engelhardt Institute of Molecular BiologyRussian Academy of SciencesMoscowRussia
  3. 3.Nikita Botanical Gardens - National Scientific CenterYaltaRussia

Personalised recommendations