1887

Journal of General Virology header logo

Volume 86, Issue 3

Genetic diversity of a natural population of Free

Abstract

An analysis of nucleotide sequences in five coding and one non-coding genomic regions of 35 (CYSDV) isolates collected on a local scale over an 8 year period is reported here. In total, 2277 nt were sequenced for each isolate, representing about 13 % of the complete virus genome. Mean nucleotide diversity for the whole population in synonymous positions in the coding regions was 0·00068, whilst in the 5′ untranslated region (5′ UTR) of genomic RNA2, it was 0·00074; both of these values are very small, compared with estimates of nucleotide diversity for populations of other plant viruses. Nucleotide diversity was also determined independently for each of the ORFs and for the 5′ UTR of RNA2; the data showed that variability is not distributed evenly among the different regions of the viral genome, with the coat protein gene showing more diversity than the other four coding regions that were analysed. However, the low variability found precluded any inference of selection differences among gene regions. On the other hand, no evidence of selection associated with host adaptation was found. In contrast, at least a single amino acid change in the coat protein appears to have been selected with time.

  • Received:
  • Accepted:
  • Published Online:
SGM
Loading

Article metrics loading...

/content/journal/jgv/10.1099/vir.0.80584-0
2005-03-01
2024-04-24
Loading full text...

Full text loading...

/deliver/fulltext/jgv/86/3/vir860815.html?itemId=/content/journal/jgv/10.1099/vir.0.80584-0&mimeType=html&fmt=ahah

References

  1. Abou-Jawdah Y., Sobh H., Fayad A., Lecoq H., Delécolle B., Trad-Ferré J. 2000; Cucurbit yellow stunting disorder virus – a new threat to cucurbits in Lebanon. J Plant Pathol 82:55–60
     [Google Scholar]
  2. Aguilar J. M., Franco M., Marco C. F., Berdiales B., Rodriguez-Cerezo E., Truniger V., Aranda M. A. 2003; Further variability within the genus Crinivirus , as revealed by determination of the complete RNA genome sequence of Cucurbit yellow stunting disorder virus . J Gen Virol 84:2555–2564 [CrossRef]
     [Google Scholar]
  3. Aranda M. A., Fraile A., Dopazo J., Malpica J. M., García-Arenal F. 1997; Contribution of mutation and RNA recombination to the evolution of a plant pathogenic RNA. J Mol Evol 44:81–88 [CrossRef]
     [Google Scholar]
  4. Ayllón M. A., Rubio L., Moya A., Guerri J., Moreno P. 1999; The haplotype distribution of two genes of citrus tristeza virus is altered after host change or aphid transmission. Virology 255:32–39 [CrossRef]
     [Google Scholar]
  5. Banks G. K., Green R. L., Cerezo E. R., Louro D., Markham P. G. 1998; Use of RAPD-PCR to characterize whitefly species in the Iberia peninsula. In Proceedings of the International Workshop on Bemisia Geminiviruses, 2nd Organising Committee p– L18 San Juan, Puerto Rico
    [Google Scholar]
  6. Bruyere A., Wantroba M., Flasinski S., Dzianott A., Bujarski J. J. 2000; Frequent homologous recombination events between molecules of one RNA component in a multipartite RNA virus. J Virol 74:4214–4219 [CrossRef]
     [Google Scholar]
  7. Célix A., Lopez-Sese A., Almarza N., Gomez-Guillamon M. L., Rodriguez-Cerezo E. 1996; Characterization of Cucurbit yellow stunting disorder virus , a Bemisia tabaci -transmitted closterovirus. Phytopathology 86:1370–1376
     [Google Scholar]
  8. Desbiez C., Lecoq H., Aboulama S., Peterschmitt M. 2000; First report of Cucurbit yellow stunting disorder virus in Morocco. Plant Dis 84:596
     [Google Scholar]
  9. Desbiez C., Wipf-Scheibel C., Lecoq H. 2002; Biological and serological variability, evolution and molecular epidemiology of Zucchini yellow mosaic virus (ZYMV, Potyvirus ) with special reference to Caribbean islands. Virus Res 85:5–16 [CrossRef]
     [Google Scholar]
  10. Díaz J. A., Nieto C., Moriones E., Truniger V., Aranda M. A. 2004; Molecular characterization of a Melon necrotic spot virus strain that overcomes the resistance in melon and nonhost plants. Mol Plant Microbe Interact 17:668–675 [CrossRef]
     [Google Scholar]
  11. Drake J. W., Holland J. J. 1999; Mutation rates among RNA viruses. Proc Natl Acad Sci U S A 96:13910–13913 [CrossRef]
     [Google Scholar]
  12. Elena S. F., Dávila M., Novella I. S., Holland J. J., Domingo E., Moya A. 1998; Evolutionary dynamics of fitness recovery from the debilitating effects of Muller's ratchet. Evolution 52:309–314 [CrossRef]
     [Google Scholar]
  13. Fitch W. M., Leiter J. M. E., Li X., Palese P. 1991; Positive Darwinian evolution in human influenza A viruses. Proc Natl Acad Sci U S A 88:4270–4274 [CrossRef]
     [Google Scholar]
  14. Fraile A., Malpica J. M., Aranda M. A., Rodríguez-Cerezo E., García-Arenal F. 1996; Genetic diversity in tobacco mild green mosaic tobamovirus infecting the wild plant Nicotiana glauca . Virology 223:148–155 [CrossRef]
     [Google Scholar]
  15. Fraile A., Alonso-Prados J. L., Aranda M. A., Bernal J. J., Malpica J. M., García-Arenal F. 1997a; Genetic exchange by recombination or reassortment is infrequent in natural populations of a tripartite RNA plant virus. J Virol 71:934–940
     [Google Scholar]
  16. Fraile A., Escriu F., Aranda M. A., Malpica J. M., Gibbs A. J., García-Arenal F. 1997b; A century of tobamovirus evolution in an Australian population of Nicotiana glauca . J Virol 71:8316–8320
     [Google Scholar]
  17. 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]
  18. Hassan A. A., Duffus J. E. 1991; A review of a yellowing and stunting disorder of cucurbits in the United Arab Emirates. Emir J Agric Sci 2:1–16
     [Google Scholar]
  19. Ina Y., Gojobori T. 1994; Statistical analysis of nucleotide sequences of the hemagglutinin gene of human influenza A viruses. Proc Natl Acad Sci U S A 91:8388–8392 [CrossRef]
     [Google Scholar]
  20. Kao J., Jia L., Tian T., Rubio L., Falk B. W. 2000; First report of Cucurbit yellow stunting disorder virus (genus Crinivirus ) in North America. Plant Dis 84:101
     [Google Scholar]
  21. Karasev A. V. 2000; Genetic diversity and evolution of closteroviruses. Annu Rev Phytopathol 38:293–324 [CrossRef]
     [Google Scholar]
  22. Kimura M. 1980; A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120 [CrossRef]
     [Google Scholar]
  23. Kumar S., Tamura K., Jakobsen I. B., Nei M. 2001; mega2: molecular evolutionary genetic analysis software. Bioinformatics 17:1244–1245 [CrossRef]
     [Google Scholar]
  24. Li W.-H. 1993; Unbiased estimation of the rates of synonymous and nonsynonymous substitution. J Mol Evol 36:96–99 [CrossRef]
     [Google Scholar]
  25. Liu H.-Y., Wisler G. C., Duffus J. E. 2000; Particle lengths of whitefly-transmitted criniviruses. Plant Dis 84:803–805 [CrossRef]
     [Google Scholar]
  26. Louro D., Vicente M., Vaira A. M., Accotto G. P., Nolasco G. 2000; Cucurbit yellow stunting disorder virus (genus Crinivirus ) associated with the yellowing disease of cucurbit crops in Portugal. Plant Dis 84:1156
     [Google Scholar]
  27. Malpica J. M., Fraile A., Moreno I., Obies C. I., Drake J. W., García-Arenal F. 2002; The rate and character of spontaneous mutation in an RNA virus. Genetics 162:1505–1511
     [Google Scholar]
  28. Marco C. F., Aguilar J. M., Abad J., Gómez-Guillamón M. L., Aranda M. A. 2003; Melon resistance to Cucurbit yellow stunting disorder virus is characterized by reduced virus accumulation. Phytopathology 93:844–852 [CrossRef]
     [Google Scholar]
  29. Martelli G. P., Agranovsky A. A., Bar-Joseph M. 15 other authors 2000; Family Closteroviridae . In Virus Taxonomy: Seventh Report of the International Committee on Taxonomy of Viruses . pp  943–952 Edited by van Regenmortel M. H. V., Fauquet C. M., Bishop D. H. L., Carstens E. B., Estes M. K., Lemon S. M., Maniloff J., Mayo M. A., McGeoch D. J., Pringle C. R., Wickner R. B. San Diego, CA: Academic Press;
  30. 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]
  31. Moreno I. M., Thompson J. R., García-Arenal F. 2004; Analysis of the systemic colonization of cucumber plants by Cucumber green mottle mosaic virus . J Gen Virol 85:749–759 [CrossRef]
     [Google Scholar]
  32. Moriones E., Fraile A., García-Arenal F. 1991; Host-associated selection of sequence variants from a satellite RNA of Cucumber mosaic virus . Virology 184:465–468 [CrossRef]
     [Google Scholar]
  33. Moya A., Rodríguez-Cerezo E., García-Arenal F. 1993; Genetic structure of natural populations of the plant RNA virus tobacco mild green mosaic virus. Mol Biol Evol 10:449–456
     [Google Scholar]
  34. Moya A., Guirao P., Cifuentes D., Beitia F., Cenis J. L. 2001; Genetic diversity of Iberian populations of Bemisia tabaci (Hemiptera: Aleyrodidae) based on random amplified polymorphic DNA-polymerase chain reaction. Mol Ecol 10:891–897 [CrossRef]
     [Google Scholar]
  35. Nei M. 1987 Molecular Evolutionary Genetics New York: Columbia University Press;
     [Google Scholar]
  36. Nei M., Gojobori T. 1986; Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol 3:418–426
     [Google Scholar]
  37. Nei M., Kumar S. 2000 Molecular Evolution and Phylogenetics New York: Oxford University Press;
     [Google Scholar]
  38. 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]
  39. 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]
  40. Rubio L., Ayllón M. A., Kong P., Fernández A., Polek M., Guerri J., Moreno P., Falk B. W. 2001a; 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]
  41. Rubio L., Abou-Yawdah Y., Lin H.-X., Falk B. W. 2001b; Geographically distant isolates of the crinivirus Cucurbit yellow stunting disorder virus show very low genetic diversity in the coat protein gene. J Gen Virol 82:929–933
     [Google Scholar]
  42. Sambrook J., Russell D. 2000 Molecular Cloning: a Laboratory Manual , 3rd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory;
     [Google Scholar]
  43. Sánchez-Campos S., Díaz J. A., Monci F., Bejarano E. R., Reina J., Navas-Castillo J., Aranda M. A., Moriones E. 2002; High genetic stability of the begomovirus Tomato yellow leaf curl Sardinia virus in southern Spain over an 8-year period. Phytopathology 92:842–849 [CrossRef]
     [Google Scholar]
  44. 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]
  45. Tian T., Rubio L., Yeh H.-H., Crawford B., Falk B. W. 1999; Lettuce infectious yellows virus: in vitro acquisition analysis using partially purified virions and the whitefly Bemisia tabaci . J Gen Virol 80:1111–1117
     [Google Scholar]
  46. Wisler G. C., Duffus J. E., Liu H.-Y., Li R. H. 1998; Ecology and epidemiology of whitefly-transmitted closteroviruses. Plant Dis 82:270–280 [CrossRef]
     [Google Scholar]
  47. Yang Z., Bielawski J. P. 2000; Statistical methods for detecting molecular adaptation. Trends Ecol Evol 15:496–503 [CrossRef]
     [Google Scholar]
  48. Zuker M. 1989; On finding all suboptimal foldings of an RNA molecule. Science 244:48–52 [CrossRef]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/jgv/10.1099/vir.0.80584-0
Loading
Genetic diversity of a natural population of Cucurbit yellow stunting disorder virus
J. Gen. Virol. 86, 815 (2005); https://doi.org/10.1099/vir.0.80584-0
/content/journal/jgv/10.1099/vir.0.80584-0
/content/journal/jgv/10.1099/vir.0.80584-0
Loading

Data & Media loading...

Most cited Most Cited RSS feed

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