1887

Abstract

At present isolates of (HSVd) are divided into five groups: three major groups (plum-type, hop-type and citrus-type) each containing isolates from only a limited number of isolation hosts and two minor groups that were presumed to derive from recombination events between members of the main groups. In this work we present the characterization of 16 new sequence variants of HSVd obtained from four Mediterranean countries (Cyprus, Greece, Morocco and Turkey) where this viroid had not previously been described. Molecular variability comparisons considering the totality of the sequence variants characterized so far revealed that most of the variability is found in the pathogenic and variable domains of the viroid molecule whereas both the terminal right (T) and left (T) domains are regions of low or no variability, respectively, suggesting the existence of constraints limiting the heterogeneity of the sequence variants. Phylogenetic analyses revealed that sequence variants belonging to the two minor recombinant subgroups are more frequent than previously thought. When the cruciform structure alternative to the typical rod-like conformation was considered it was observed that the upper part of this structure (hairpin I) was strictly conserved whereas in the lower part a reduced variability was found. The existence of a covariation in this lower part was notable. Interestingly, a hammerhead-like sequence was found within the T domain of HSVd and it was strictly conserved in all the sequence variants. The evolutionary implications of the presence of this motif on the HSVd are discussed.

Loading

Article metrics loading...

/content/journal/jgv/10.1099/0022-1317-82-4-953
2001-04-01
2024-03-28
Loading full text...

Full text loading...

/deliver/fulltext/jgv/82/4/0820953a.html?itemId=/content/journal/jgv/10.1099/0022-1317-82-4-953&mimeType=html&fmt=ahah

References

  1. Amari K., Cañizares M. C., Myrta A., Sabanadzovic S., Srhiri M., Gavriel I., çaglayan K., Varveri C., Gatt M., Di Terlizzi B., Pallás V. 2000; First report on hop stunt viroid (HSVd) from some Mediterranean countries. Phytopathologia Mediterranea 39:271–276
    [Google Scholar]
  2. Ambrós S., Hernández C., Desvignes J. C., Flores R. 1998; Genomic structure of three phenotypically different isolates of peach latent mosaic viroid: implications of the existence of constraints limiting the heterogeneity of viroid quasispecies. Journal of Virology 72:7397–7406
    [Google Scholar]
  3. Astruc N., Marcos J. F., Macquaire G., Candresse T., Pallás V. 1996; Studies on the diagnosis of hop stunt viroid in fruit trees: identification of new hosts and application of a nucleic acid extraction procedure based on non-organic solvents. European Journal of Plant Pathology 102:837–846
    [Google Scholar]
  4. Bracho M. A., Moya A., Barrio E. 1998; Contribution of Taq polymerase-induced errors to the estimation of RNA virus diversity. Journal of General Virology 79:2921–2928
    [Google Scholar]
  5. Candresse T., Revers F., Le Gall O., Kofalvi S., Marcos J., Pallás V. 1997; Systematic search for recombination events in plant viruses and viroids. In Virus Resistant Transgenic Plants: Potential Ecological Impact pp 20–25 Edited by Tepfer M., Balázs E. Berlin: Springer-Verlag;
    [Google Scholar]
  6. Cañizares M., Marcos J., Pallás V. 1998; Studies on the incidence of hop stunt viroid in apricot trees by using an easy and short extraction method to analyze a large number of plants. Acta Horticulturae 472:581–585
    [Google Scholar]
  7. Cañizares M., Marcos J., Pallás V. 1999; Molecular characterization of an almond isolate of hop stunt viroid (HSVd) and conditions for eliminating spurious hybridization in its diagnostics in almond samples. European Journal of Plant Pathology 105:553–558
    [Google Scholar]
  8. Collins R. F., Gellatly D. L., Sehgal O. P., Abouhaidar M. G. 1998; Self-cleaving circular RNA associated with rice yellow mottle virus is the smallest viroid-like RNA. Virology 241:269–275
    [Google Scholar]
  9. Diener T. 1991; Subviral pathogens of plants: viroids and viroidlike satellite RNAs. FASEB Journal 5:2808–2813
    [Google Scholar]
  10. Diener T. 1996; Origin and evolution of viroids and viroid-like satellite RNAs. Virus Genes 11:119–131
    [Google Scholar]
  11. Diener T., Smith D., Hammond R., Albanese G., La Rosa R., Davino M. 1988; Citrus B viroid identified as a strain of hop stunt viroid. Plant Disease 72:691–693
    [Google Scholar]
  12. Durán-Vila N., Roistacher C. N., Rivera-Bustamante R., Semancik J. S. 1988; A definition of citrus viroid groups and their relationship to the exocortis disease. Journal of General Virology 69:3069–3080
    [Google Scholar]
  13. Elena S. F., Dopazo J., Flores R., Diener T. O., Moya A. 1991; Phylogeny of viroids, viroid like satellite RNAs, and the viroid like domain of hepatitis δ virus RNA. Proceedings of the National Academy of Sciences, USA 88:5631–5634
    [Google Scholar]
  14. Felsenstein J. 1993 PHYLIP (Phylogeny Inference Package) version 3.5c. Distributed by the author Department of Genetics, University of Washington; Seattle, USA:
    [Google Scholar]
  15. Flores R., Di Serio F., Hernández C. 1997; Viroids: the non coding genomes. Seminars in Virology 8:65–73
    [Google Scholar]
  16. Flores R., Randles J., Bar-Joseph M., Diener T. 1998; A proposed scheme for viroid classification and nomenclature. Archives of Virology 143:623–629
    [Google Scholar]
  17. Hernández C., Flores R. 1992; Plus and minus RNAs of peach latent mosaic self-cleavage in vitro via hammerhead structures. Proceedings of the National Academy of Sciences, USA 89:3711–3715
    [Google Scholar]
  18. Hertel K. J., Pardi A., Uhlenbeck O. C., Koizumi M., Ohtsuka E., Uesugi S., Cedergen R., Eckstein F., Gerlach W. L., Hodgson R., Symons R. H. 1992; Numbering system for the hammerhead. Nucleic Acids Research 20:3252
    [Google Scholar]
  19. Hsu Y., Chen W., Owens R. A. 1994; Nucleotide sequence of a hop stunt viroid variant isolated from citrus growing in Taiwan. Virus Genes 9:193–195
    [Google Scholar]
  20. Hu Y., Feldstein P. A., Hammond J., Hammond R. W., Bottino P. J., Owens R. A. 1997; Destabilization of potato spindle tuber viroid by mutations in the left terminal loop. Journal of General Virology 78:1199–1206
    [Google Scholar]
  21. Keese P., Symons R. H. 1985; Domains in viroids: evidence of intermolecular RNA rearrangements and their contribution to viroid evolution. Proceedings of the National Academy of Sciences, USA 82:4582–4586
    [Google Scholar]
  22. Keese P., Visvader J., Symons R. 1988; Sequence variability in plant viroid RNAs. In RNA Genetics pp 71–98 Edited by Domingo E., Holland J., Ahlquist P. Boca Raton: CRC Press;
    [Google Scholar]
  23. Kofalvi S. A., Marcos J. F., Cañizares M. C., Pallás V., Candresse T. 1997; Hop stunt viroid (HSVd) sequence variants from Prunus species: evidence for recombination between HSVd isolates. Journal of General Virology 78:3177–3186
    [Google Scholar]
  24. Koltunow A. M., Rezaian M. A. 1988; Grapevine yellow speckle viroid: structural features of a new viroid group. Nucleic Acids Research 16:849–864
    [Google Scholar]
  25. Liu Y.-H., Symons R. 1998; Specific RNA self-cleavage in coconut cadang cadang viroid: potential for a role in rolling circle replication. RNA 4:418–429
    [Google Scholar]
  26. Ohno T., Takamatsu N., Meshi T., Okada Y. 1983; Hop stunt viroid: molecular cloning and nucleotide sequence of the complete cDNA copy. Nucleic Acids Research 11:6185–6196
    [Google Scholar]
  27. Pallás V., Navarro A., Flores R. 1987; Isolation of a viroid-like RNA from hop different from hop stunt viroid. Journal of General Virology 68:3201–3205
    [Google Scholar]
  28. Pallás V., Más P., Sánchez-Navarro J. A. 1998; Detection of plant RNA viruses by non-isotopic dot-blot hybridization. In Plant Virus Protocols: from Virus Isolation to Transgenic Resistance pp 461–468 Edited by Foster G., Taylor S. Totowa, NY, USA: Humana Press;
    [Google Scholar]
  29. Pelchat M., Lévesque D., Ouellet J., Laurendeau S., Lévesque S., Lehoux J., Thompson D. A., Eastwell K. C., Skrzeczkowski L. J., Perreault J. P. 2000; Sequencing of peach latent mosaic viroid variants from nine North American peach cultivars shows that this RNA folds into a complex secondary structure. Virology 271:37–45
    [Google Scholar]
  30. Polivka H., Staub U., Gross H. J. 1996; Variation of viroid profiles in individual grapevine plants: novel grapevine yellow speckle viroid 1 mutants show alterations of hairpin I. Journal of General Virology 77:155–161
    [Google Scholar]
  31. Reanwarakorn K., Semancik J. S. 1998; Regulation of pathogenicity in hop stunt viroid-related group II citrus viroids. Journal of General Virology 79:3163–3171
    [Google Scholar]
  32. Reanwarakorn K., Semancik J. S. 1999; Correlation of hop stunt viroid variants to cachexia and xiloporosis diseases of citrus. Phytopathology 89:568–574
    [Google Scholar]
  33. Sano T., Ishiguro A. 1998; Viability and pathogenicity of intersubgroup viroid chimeras suggest possible involvement of the terminal right region in the replication. Virology 240:238–244
    [Google Scholar]
  34. Sano T., Hataya T., Terai Y., Shikata E. 1989; Hop stunt viroid strains from dapple fruit disease of plum and peach in Japan. Journal of General Virology 70:1311–1319
    [Google Scholar]
  35. Semancik J. S. 1987 Viroids and Viroid-like Pathogens Boca Raton: CRC Press;
  36. Semancik J. S., Roistacher C. N., Rivera-Bustamante R., Durán-Vila N. 1988; Citrus cachexia viroid, a new viroid of citrus: relationship to viroids of the exocortis disease complex. Journal of General Virology 69:3059–3068
    [Google Scholar]
  37. Shikata E. 1990; New viroids from Japan. Seminars in Virology 1:107–115
    [Google Scholar]
  38. Symons R. H. 1997; Plant pathogenic RNAs and RNA catalysis. Nucleic Acids Research 25:2683–2689
    [Google Scholar]
  39. 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 Research 22:4673–4680
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/jgv/10.1099/0022-1317-82-4-953
Loading
/content/journal/jgv/10.1099/0022-1317-82-4-953
Loading

Data & Media loading...

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