1887

Abstract

The genetic variability and population structure of a collection of 45 (GLRaV-3) isolates were studied by single-stranded conformation polymorphism (SSCP) and sequence analysis of the RNA-dependent RNA polymerase (RdRp), heat-shock protein 70 homologue (HSP-70) and coat protein (CP) genes. The distribution of SSCP profiles was not correlated with the geographical origin of the isolates, indicating that GLRaV-3 is a single, undifferentiated population. The majority of the isolates showed an SSCP profile and a population structure that were composed of a single predominant variant. However, 10 % of the isolates for the RdRp and HSP-70 genes and 15 % for the CP gene were composed of a combination of two or more variants. Estimation of genetic diversity and phylogenetic analysis disclosed the possible existence of vines with mixed infections by diverging sequence variants, showing, in some cases, possible recombination events. Furthermore, differences in the genetic diversity and constraints existing in the three regions analysed indicated a higher variability in the CP gene. The epidemiological and biological implications of this finding are discussed.

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2005-01-01
2019-11-22
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References

  1. Beidler, J. L., Hilliard, P. R. & Rill, R. L. ( 1982; ). Ultrasensitive staining of nucleic acids with silver. Anal Biochem 126, 374–380.[CrossRef]
    [Google Scholar]
  2. Bracho, M. A., Moya, A. & Barrio, E. ( 1998; ). Contribution of Taq polymerase-induced errors to the estimation of RNA virus diversity. J Gen Virol 79, 2921–2928.
    [Google Scholar]
  3. Bradley, R. D. & Hillis, D. M. ( 1997; ). Recombinant DNA sequences generated by PCR amplification. Mol Biol Evol 14, 592–593.[CrossRef]
    [Google Scholar]
  4. Devereux, J., Haerbeli, P. & Smithies, O. ( 1984; ). A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res 12, 387–395.[CrossRef]
    [Google Scholar]
  5. Fajardo, T. V. M., Kuhn, G. B., Eiras, M. & Nickel, O. ( 2001; ). Partial characterization of an isolate of grapevine leafroll associated virus 3 in grape virus 3. Fitopatol Bras 26, 505–511.
    [Google Scholar]
  6. Foissac, X., Svanella-Dumas, L., Dulucq, M. J., Candresse, T. & Gentit, P. ( 2000; ). Polyvalent detection of fruit tree tricho, capillo and foveaviruses by nested RT-PCR using degenerated and inosine containing primers (PDO RT-PCR). Acta Hort 550, 37–44.
    [Google Scholar]
  7. García-Arenal, F., Fraile, A. & Malpica, J. M. ( 2001; ). Variability and genetic structure of plant virus populations. Annu Rev Phytopathol 39, 157–186.[CrossRef]
    [Google Scholar]
  8. Gugerli, P. ( 2003; ). Grapevine leafroll and related viruses. In Extended Abstracts of the XIV Meeting of the International Council for the Study of Virus and Virus-like Diseases of the Grapevine, Locorotondo, Italy, 12–17 September 2003.
  9. Habili, N., Fazeli, C. F., Ewart, A., Hamilton, R., Cirami, R., Saldarelli, P., Minafra, A. & Rezaian, A. ( 1995; ). Natural spread and molecular analysis of grapevine leafroll-associated virus 3 in Australia. Phytopathology 85, 1418–1422.[CrossRef]
    [Google Scholar]
  10. Holland, J. J., De La Torre, J. C. & Steinhauer, D. A. ( 1992; ). RNA virus populations as quasispecies. Curr Top Microbiol Immunol 176, 1–20.
    [Google Scholar]
  11. Jukes, T. H. & Cantor, C. R. ( 1969; ). Evolution of protein molecules. In Mammalian Protein Metabolism, pp. 21–132. Edited by H. N. Munro. New York: Academic Press.
  12. Karasev, A. V. ( 2000; ). Genetic diversity and evolution of closteroviruses. Annu Rev Phytopathol 38, 293–324.[CrossRef]
    [Google Scholar]
  13. Kong, P., Rubio, L., Polek, M. & Falk, B. W. ( 2000; ). Population structure and genetic diversity within California Citrus tristeza virus (CTV) isolates. Virus Genes 21, 139–145.[CrossRef]
    [Google Scholar]
  14. Kumar, S., Tamura, K., Jakobsen, I. B. & Nei, M. ( 2001; ). mega2: molecular evolutionary genetic analysis software. Bioinformatics 17, 1244–1245.[CrossRef]
    [Google Scholar]
  15. Li, W.-H. ( 1993; ). Unbiased estimation of the rates of synonymous and nonsynonymous substitution. J Mol Evol 36, 96–99.[CrossRef]
    [Google Scholar]
  16. Lin, H.-X., Rubio, L., Smythe, A., Jiminez, M. & Falk, B. W. ( 2003; ). Genetic diversity and biological variation among California isolates of Cucumber mosaic virus. J Gen Virol 84, 249–258.[CrossRef]
    [Google Scholar]
  17. Ling, K.-S., Zhu, H.-Y., Alvizo, H., Hu, J. S., Drong, R. F., Slightom, J. L. & Gonsalves, D. ( 1997; ). The coat protein gene of grapevine leafroll associated closterovirus-3: cloning, nucleotide sequencing and expression in transgenic plants. Arch Virol 142, 1101–1116.[CrossRef]
    [Google Scholar]
  18. Ling, K.-S., Zhu, H.-Y., Drong, R. F., Slightom, J. L., McFerson, J. R. & Gonsalves, D. ( 1998; ). Nucleotide sequence of the 3′-terminal two-thirds of the grapevine leafroll-associated virus-3 genome reveals a typical monopartite closterovirus. J Gen Virol 79, 1299–1307.
    [Google Scholar]
  19. Ling, K.-S., Krastanova, T., Xue, B., Zhu, H.-Y., Meng, B. & Gonsalves, D. ( 2000; ). Complete genome sequence of grapevine leafroll associated virus-3 and development of transgenic plants expressing its genes. In Extended Abstracts of the XIII Meeting of the International Council for the Study of Virus and Virus-like Diseases of the Grapevine, Adelaide, Australia, 12–17 March 2000.
  20. Lynch, M. & Crease, T. J. ( 1990; ). The analysis of population survey data on DNA sequence variation. Mol Biol Evol 7, 377–394.
    [Google Scholar]
  21. Martelli, G. P. ( 2003; ). Grapevine virology highlights 2000–2003. In Extended Abstracts of the XIV Meeting of the International Council for the Study of Virus and Virus-like Diseases of the Grapevine, Locorotondo, Italy, 12–17 September 2003.
  22. Martelli, G. P., Agranovsky, A. A., Bar-Joseph, M. & 13 other authors ( 2002; ). The family Closteroviridae revised. Arch Virol 147, 2039–2044.[CrossRef]
    [Google Scholar]
  23. Negroni, M. & Buc, H. ( 2001; ). Mechanisms of retroviral recombination. Annu Rev Genet 35, 275–302.[CrossRef]
    [Google Scholar]
  24. Orita, M., Suzuki, T., Sekiya, T. & Hayashi, K. ( 1989; ). Rapid and sensitive detection of point mutations and genetic polymorphisms using the polymerase chain reaction. Genomics 5, 874–879.[CrossRef]
    [Google Scholar]
  25. Palacio, A. & Duran-Vila, N. ( 1999; ). Single-strand conformation polymorphism (SSCP) analysis as a tool for viroid characterisation. J Virol Methods 77, 27–36.[CrossRef]
    [Google Scholar]
  26. Pamilo, P. & Bianchi, N. O. ( 1993; ). Evolution of the Zfx and Zfy genes: rates and interdependence between the genes. Mol Biol Evol 10, 271–281.
    [Google Scholar]
  27. Rosciglione, B. & Gugerli, P. ( 1986; ). Maladies de l'enroulement et bois strié, de la vigne: analyse microscopique et sérologique. Rev Suisse Vitic Arboric Hortic 18, 207–211 (in French).
    [Google Scholar]
  28. Rubio, L., Soong, J., Kao, J. & Falk, B. W. ( 1999; ). Geographic distribution and molecular variation of isolates of three whitefly-borne closteroviruses of cucurbits: lettuce infectious yellows virus, cucurbit yellow stunting disorder virus, and beet pseudo-yellows virus. Phytopathology 89, 707–711.[CrossRef]
    [Google Scholar]
  29. Rubio, L., Ayllón, M. A., Kong, P., Fernández, A., Polek, M., Guerri, J., Moreno, P. & Falk, B. W. ( 2001; ). Genetic variation of Citrus tristeza virus isolates from California and Spain: evidence for mixed infections and recombination. J Virol 75, 8054–8062.[CrossRef]
    [Google Scholar]
  30. Saitou, N. & Nei, M. ( 1987; ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–425.
    [Google Scholar]
  31. Saldarelli, P., Rowhani, A., Routh, G., Minafra, A. & Digiaro, M. ( 1998; ). Use of degenerate primers in a RT-PCR assay for the identification and analysis of some filamentous viruses, with special reference to clostero- and vitiviruses of the grapevine. Eur J Plant Pathol 104, 945–950.[CrossRef]
    [Google Scholar]
  32. Sambrook, J., Fritsch, E. F. & Maniatis, T. ( 1989; ). Molecular Cloning: a Laboratory Manual, 2nd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory.
  33. Sforza, R., Komar, V. & Greif, C. ( 2000; ). New scale insect vectors of grapevine closteroviruses. In Extended Abstracts of the XIII Meeting of the International Council for the Study of Virus and Virus-like Diseases of the Grapevine, Adelaide, Australia, 12–17 March 2000.
  34. Sokal, R. R. & Rohlf, F. J. ( 1993; ). Biometry: the Principles and Practice of Statistics in Biological Research, 3rd edn. New York: W. H. Freeman.
  35. Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F. & Higgins, D. G. ( 1997; ). The clustal_x windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25, 4876–4882.[CrossRef]
    [Google Scholar]
  36. Turturo, C., Rott, M. E., Minafra, A., Saldarelli, P., Jelkmann, W. & Martelli, G. P. ( 2000; ). Grapevine leafroll-associated virus 1: partial cloning and RT-PCR detection. In Extended Abstracts of the XIII Meeting of the International Council for the Study of Virus and Virus-like Diseases of the Grapevine, Adelaide, Australia, March 12–17 2000.
  37. Weiller, G. F. ( 1998; ). Phylogenetic profiles: a graphical method for detecting genetic recombinations in homologous sequences. Mol Biol Evol 15, 326–335.[CrossRef]
    [Google Scholar]
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