1887

Abstract

The nematode-borne , from the genus in the family , causes severe degeneration of grapevines in most vineyards worldwide. We characterized 347 isolates from transgenic and conventional grapevines from two vineyard sites in the Champagne region of France for their molecular variant composition. The population structure and genetic diversity were examined in the coat protein gene by IC-RT-PCR-RFLP analysis with RI and I, and nucleotide sequencing, respectively. RFLP data suggested that 55 % (191 of 347) of the isolates had a population structure consisting of one predominant variant. Sequencing data of 51 isolates representing the different restrictotypes confirmed the existence of mixed infection with a frequency of 33 % (17 of 51) and showed two major predominant haplotypes representing 71 % (60 of 85) of the sequence variants. Comparative nucleotide diversity among population subsets implied a lack of genetic differentiation according to host (transgenic vs conventional) or field site for most restrictotypes (17 of 18 and 13 of 18) and for haplotypes in most phylogenetic groups (seven of eight and six of eight), respectively. Interestingly, five of the 85 haplotypes sequenced had an intermediate divergence (0·036–0·066) between the lower (0·005–0·028) and upper range (0·083–0·138) of nucleotide variability, suggesting the occurrence of homologous RNA recombination. Sequence alignments clearly indicated a mosaic structure for four of these five variants, for which recombination sites were identified and parental lineages proposed. This is the first in-depth characterization of the population structure and genetic diversity in a nepovirus.

Loading

Article metrics loading...

/content/journal/jgv/10.1099/vir.0.79904-0
2004-08-01
2024-11-12
Loading full text...

Full text loading...

/deliver/fulltext/jgv/85/8/vir852435.html?itemId=/content/journal/jgv/10.1099/vir.0.79904-0&mimeType=html&fmt=ahah

References

  1. Aaziz R., Tepfer M. 1999; Recombination in RNA viruses and in virus-resistant transgenic plants. J Gen Virol 80:1339–1346
    [Google Scholar]
  2. Albiach-Marti M. R., Mawassi M., Gowda S. 11 other authors 2000; Sequences of Citrus tristeza virus separated in time and space are essentially identical. J Virol 74:6856–6865 [CrossRef]
    [Google Scholar]
  3. Andret-Link P., Schmitt-Keichinger C., Demangeat G., Komar V., Fuchs M. 2004; The specific transmission of Grapevine fanleaf virus by its nematode vector Xiphinema index is solely determined by the viral coat protein. Virology 320:12–22 [CrossRef]
    [Google Scholar]
  4. Azzam O., Yambao M. L. M., Muhsin M., McNally K. L., Umadhay K. M. L. 2000; Genetic diversity of rice tungro spherical virus in tungro-endemic provinces of the Philippines and Indonesia. Arch Virol 145:1183–1197 [CrossRef]
    [Google Scholar]
  5. Belin C., Schmitt C., Gaire F., Walter B., Demangeat G., Pinck L. 1999; The nine C-terminal residues of grapevine fanleaf nepovirus movement protein are critical for systemic virus spread. J Gen Virol 80:1347–1356
    [Google Scholar]
  6. Brandt S., Ibl M., Himmler G. 1995; Coat protein gene sequence of an Austrian isolate of grapevine fanleaf virus. Arch Virol 140:157–164 [CrossRef]
    [Google Scholar]
  7. Chandrasekar V., Johnson J. E. 1998; The structure of tobacco ringspot virus: a link in the evolution of icosahedral capsids in the picornavirus superfamily. Structure 6:157–171 [CrossRef]
    [Google Scholar]
  8. Fajardo T. V. M., Kuhn G. B., Eiras M., Nickel O. 2001; Partial characterization of an isolate of Grapevine fanleaf virus. Fitopatol Bras 26:505–511
    [Google Scholar]
  9. Fraile A., Malpica J. M., Aranda M. A., Rodriguez-Cerezo E., Garcia-Arenal F. 1996; Genetic diversity in tobacco mild green mosaic tobamovirus infecting the wild plant Nicotiana glauca . Virology 223:148–155 [CrossRef]
    [Google Scholar]
  10. Gaire F., Schmitt C., Stussi-Garaud C., Pinck L., Ritzenthaler C. 1999; Protein 2A of grapevine fanleaf nepovirus is implicated in RNA2 replication and colocalizes to the replication site. Virology 264:25–36 [CrossRef]
    [Google Scholar]
  11. Garcia-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]
  12. Gibbs M. J., Armstrong J. S., Gibbs A. J. 2000; Sister-scanning: a Monte Carlo procedure for assessing signals in recombinant sequences. Bioinformatics 16:573–582 [CrossRef]
    [Google Scholar]
  13. Glais L., Tribodet M., Kerlan C. 2002; Genomic variability in Potato potyvirus Y (PVY): evidence that PVYNW and PVYNTN variants are single to multiple recombinants between PVYO and PVYN isolates. Arch Virol 147:363–378 [CrossRef]
    [Google Scholar]
  14. Goszczynski D. E., Jooste A. E. C. 2003; Identification of grapevines infected with divergent variants of Grapevine virus A using variant-specific RT-PCR. J Virol Methods 112:157–164 [CrossRef]
    [Google Scholar]
  15. Guyader S., Giblot Ducray D. 2002; Sequence analysis of Potato leafroll virus isolates reveals genetic stability, major evolutionary events and differential selection pressure between overlapping reading frame products. J Gen Virol 83:1799–1807
    [Google Scholar]
  16. Hancheng G., Wenqi C., Keqiang M. 1996; The cloning, sequence analysis, and expression in E. coli of coat protein gene of grapevine fanleaf virus Gh. Chin J Biotechnol 12:73–79
    [Google Scholar]
  17. Hewitt W. B., Raski D. J., Goheen A. C. 1958; Nematode vector of soil-borne fanleaf virus of grapevines. Phytopathology 48:586–595
    [Google Scholar]
  18. Huss B., Muller S., Sommermeyer G., Walter B., Van Regenmortel M. H. V. 1987; Grapevine fanleaf virus monoclonal antibodies: their use to distinguish different isolates. J Phytopathol 119:358–370 [CrossRef]
    [Google Scholar]
  19. Huss B., Walter B., Fuchs M. 1989; Cross-protection between arabis mosaic virus and grapevine fanleaf virus isolates in Chenopodium quinoa . Ann Appl Biol 114:45–60 [CrossRef]
    [Google Scholar]
  20. Le Gall O., Candresse T., Dunez J. 1995; Transfer of the 3′ non-translated region of grapevine chrome mosaic virus RNA-1 by recombination to tomato black ring virus RNA-2 in pseudorecombinant isolates. J Gen Virol 76:1285–1289 [CrossRef]
    [Google Scholar]
  21. Little A., Fazeli C. F., Rezaian M. A. 2001; Hypervariable genes in Grapevine leafroll associated virus 1 . Virus Res 80:109–116 [CrossRef]
    [Google Scholar]
  22. Martelli G. P., Savino V. 1990; Fanleaf degeneration. In Compendium of Grape Diseases pp  48–49 Edited by Pearson R., Goheen A. C. St Paul, MN, USA: APS Press;
    [Google Scholar]
  23. Mauro M. C., Toutain S., Walter B., Pinck L., Otten L., Coutos-Thevenot P., Deloire A., Barbier P. 1995; High efficiency regeneration of grapevine plants transformed with the GFLV coat protein gene. Plant Sci 112:97–106 [CrossRef]
    [Google Scholar]
  24. Mayo M. A., Robinson D. J. 1996 Nepoviruses: molecular biology and replication. In The Plant Viruses, vol. 5: Polyhedral Virions and Bipartite RNA Genomes Edited by Harrison B. D., Murant A. F. New York: Plenum Press;
    [Google Scholar]
  25. Meng B., Zhu H., Gonsalves D. 1999; Rupestris stem pitting associated virus-1 consists of a family of sequence variants. Arch Virol 144:2071–2085 [CrossRef]
    [Google Scholar]
  26. Naraghi-Arani P., Daubert S., Rowhani A. 2001; Quasispecies nature of the genome of Grapevine fanleaf virus . J Gen Virol 82:1791–1795
    [Google Scholar]
  27. Nolasco G., de Sequeira O. A. 1993; Genome diversity of field isolates of Grapevine fanleaf virus (GFLV) analyzed by single stranded conformation (SSCP) and restriction fragment length (RFLP) polymorphisms. In Extended Abstracts of the 11th Meeting of the International Council for the Study of Viruses and Virus-like Diseases of the Grapevine , 6–9 September 1993 Montreux, Switzerland: pp  31–32 Edited by Gugerli P.
    [Google Scholar]
  28. Pinck L., Fuchs M., Pinck M., Ravelonandro M., Walter B. 1988; A satellite RNA in grapevine fanleaf virus strain F13. J Gen Virol 69:233–239 [CrossRef]
    [Google Scholar]
  29. Raski D. J., Goheen A. C., Lider L. A., Meredith C. P. 1983; Strategies against grapevine fanleaf virus and its nematode vector. Plant Dis 67:335–339 [CrossRef]
    [Google Scholar]
  30. Ritzenthaler C., Viry M., Pinck M., Margis R., Fuchs M., Pinck L. 1991; Complete nucleotide sequence and genetic organization of grapevine fanleaf nepovirus RNA1. J Gen Virol 72:2357–2365 [CrossRef]
    [Google Scholar]
  31. Ritzenthaler C., Schmitt A. C., Michler P., Stussi-Garaud C., Pinck L. 1995; Grapevine fanleaf nepovirus P38 putative movement protein is located on tubules in vivo . Mol Plant–Microbe Interact 8:379–387 [CrossRef]
    [Google Scholar]
  32. Rubio L., Ayllon M. A., Kong P., Fernandez 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]
  33. Saitou N., Nei M. 1987; The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425
    [Google Scholar]
  34. Sanchez F., Chay C., Borja M. J., Rowhani A., Romero J., Bruening G., Ponz F. 1991; cDNA sequence of the capsid protein gene and 3′ untranslated region of a fanleaf isolate of grapevine fanleaf virus. Nucleic Acids Res 19:5440 [CrossRef]
    [Google Scholar]
  35. Savino V., Cherif C., Martelli G. P. 1985; A natural serological variant of grapevine fanleaf virus. Phytopathol Mediterr 24:325–328
    [Google Scholar]
  36. Serghini M. A., Fuchs M., Pinck M., Reinbolt J., Walter B., Pinck L. 1990; RNA2 of grapevine fanleaf virus: sequence analysis and coat protein cistron location. J Gen Virol 71:1433–1441 [CrossRef]
    [Google Scholar]
  37. Shi B. J., Habili N., Symons R. H. 2003; Nucleotide sequence variation in a small region of the Grapevine fleck virus replicase provides evidence for two sequence variants of the virus. Ann Appl Biol 142:349–355 [CrossRef]
    [Google Scholar]
  38. Strimmer K., von Haeseler A. 1996; Quartet puzzling: a quartet maximum-likelihood method for reconstructing tree topologies. Mol Biol Evol 13:964–969 [CrossRef]
    [Google Scholar]
  39. Szychowski J. A., McHenry M. V., Walker M. A., Walpert J. A., Credi R., Semancik J. S. 1995; The vein-banding disease syndrome: a synergistic reaction between grapevine viroids and fanleaf virus. Vitis 34:229–232
    [Google Scholar]
  40. Tamura K., Nei M. 1993; Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 10:512–526
    [Google Scholar]
  41. Thompson J. D., Higgins D. G., Gibson T. J. 1994; clustal w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680 [CrossRef]
    [Google Scholar]
  42. Vigne E., Komar V., Fuchs M. 2004; Field safety assessment of recombination in transgenic grapevines expressing the coat protein gene of Grapevine fanleaf virus . Transgenic Res 13:165–179 [CrossRef]
    [Google Scholar]
  43. Vuittenez A., Munck M. C., Kuszala J. 1964; Souches de virus à hautes aggressivité isolées de vignes atteintes de dégénérescence infectieuse. Etud Virol Appl 5:69–78 (in French
    [Google Scholar]
  44. Walter B., Etienne L. 1987; Detection of the grapevine fanleaf viruses away from the period of vegetation. J Phytopathol 120:355–364 [CrossRef]
    [Google Scholar]
  45. Wetzel T., Meunier L., Jaeger U., Reustle G. M., Krczal G. 2001; Complete nucleotide sequences of the RNAs 2 of German isolates of Grapevine fanleaf virus and Arabis mosaic nepoviruses. Virus Res 75:139–145 [CrossRef]
    [Google Scholar]
/content/journal/jgv/10.1099/vir.0.79904-0
Loading
/content/journal/jgv/10.1099/vir.0.79904-0
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error