1887

Abstract

A total of 154 partial nucleotide sequences within the (BanMMV) ORF1, which encodes the viral RNA-dependent RNA polymerase (RdRp), was obtained from 68 distinct infected banana accessions originating from various locations worldwide. The 310 nt sequences displayed a high level of variability with a mean pairwise nucleotide sequence divergence level of 20·4 %. This situation resulted essentially from a high rate of synonymous mutations. A similar analysis was performed for a limited selection of 10 banana accessions (30 sequences) on the region comprising approximately the last 310 nt of the BanMMV genome. This region corresponds to the 3′ end of ORF5, which encodes the coat protein (234 nt), and to the 3′ non-coding region. This analysis confirmed the high level of diversity observed in the RdRp dataset, characterized by a high level of synonymous mutations. Analysis of intra-host diversity indicated the existence of two distinct situations, with some plants containing only closely related sequence variants, whereas others contained widely divergent isolates. Analyses indicated that BanMMV genetic diversity is not structured by the geographical origin of the infected accessions or by their genotype. This situation may be, in part, explained by the exchange of banana germplasm between different parts of the world and also by plant-to-plant transfer of virus isolates, the evidence for which is, for the first time, provided by this study.

Loading

Article metrics loading...

/content/journal/jgv/10.1099/vir.0.81197-0
2005-11-01
2020-01-20
Loading full text...

Full text loading...

/deliver/fulltext/jgv/86/11/3179.html?itemId=/content/journal/jgv/10.1099/vir.0.81197-0&mimeType=html&fmt=ahah

References

  1. Adams, M. J., Antoniw, J. F., Bar-Joseph, M. & 7 other authors ( 2004; ). The new plant virus family Flexiviridae and assessment of molecular criteria for species demarcation. Arch Virol 149, 1045–1060.
    [Google Scholar]
  2. Chare, E. R. & Holmes, E. C. ( 2004; ). Selection pressures in the capsid genes of plant RNA viruses reflect mode of transmission. J Gen Virol 85, 3149–3157.[CrossRef]
    [Google Scholar]
  3. Domingo, E. & Holland, J. J. ( 1997; ). RNA virus mutations and fitness for survival. Annu Rev Microbiol 51, 151–178.[CrossRef]
    [Google Scholar]
  4. Domingo, E., Escarmis, C., Sevilla, N., Moya, A., Elena, S. F., Quer, J., Novella, I. S. & Holland, J. J. ( 1996; ). Basic concepts in RNA virus evolution. FASEB J 10, 859–864.
    [Google Scholar]
  5. 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]
  6. Foissac, X., Svanella-Dumas, L., Gentit, P., Dulucq, M.-J., Marais, A. & Candresse, T. ( 2005; ). Polyvalent degenerate oligonucleotides reverse transcription-polymerase chain reaction: a polyvalent detection and characterization tool for trichoviruses, capilloviruses, and foveaviruses. Phytopathology 95, 617–625.[CrossRef]
    [Google Scholar]
  7. Gambley, C. F. & Thomas, J. E. ( 2001; ). Molecular characterisation of Banana mild mosaic virus, a new filamentous virus in Musa spp. Arch Virol 146, 1369–1379.[CrossRef]
    [Google Scholar]
  8. 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]
  9. García-Arenal, F., Fraile, A. & Malpica, J. M. ( 2003; ). Variation and evolution of plant virus populations. Int Microbiol 6, 225–232.[CrossRef]
    [Google Scholar]
  10. German-Retana, S., Bergey, B., Delbos, R. P., Candresse, T. & Dunez, J. ( 1997; ). Complete nucleotide sequence of the genome of a severe cherry isolate of apple chlorotic leaf spot trichovirus (ACLSV). Arch Virol 142, 833–841.[CrossRef]
    [Google Scholar]
  11. Gibbs, A. J., Keese, P. L., Gibbs, M. J. & García-Arenal, F. ( 1999; ). Plant virus evolution: past, present and future. In Origins and Evolution of Viruses, pp. 263–285. Edited by E. Domingo, R. Webster & J. J. Holland. San Diego: Academic Press.
  12. Grenfell, B. T., Pybus, O. G., Gog, J. R., Wood, J. L. N., Daly, J. M., Mumford, J. A. & Holmes, E. C. ( 2004; ). Unifying the epidemiological and evolutionary dynamics of pathogens. Science 303, 327–332.[CrossRef]
    [Google Scholar]
  13. 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]
  14. Kimura, M. ( 1983; ). The Neutral Theory of Molecular Evolution. Cambridge, UK: Cambridge University Press.
  15. Koonin, E. V. ( 1991; ). The phylogeny of RNA-dependent RNA polymerases of positive-strand RNA viruses. J Gen Virol 72, 2197–2206.[CrossRef]
    [Google Scholar]
  16. Koonin, E. V., Choi, G. H., Nuss, D. L., Shapira, R. & Carrington, J. C. ( 1991; ). Evidence for common ancestry of a chestnut blight hypovirulence-associated double-stranded RNA and a group of positive-strand RNA plant viruses. Proc Natl Acad Sci U S A 88, 10647–10651.[CrossRef]
    [Google Scholar]
  17. Kumar, S., Tamura, K., Jakobsen, I. B. & Nei, M. ( 2001; ). mega2: molecular evolutionary genetics analysis software. Bioinformatics 17, 1244–1245.[CrossRef]
    [Google Scholar]
  18. Löve, A., Molnegren, V., Månsson, A.-S., Smáradóttir, A., Thorsteinsson, S. B. & Widell, A. ( 2004; ). Evolution of hepatitis C virus variants following blood transfusion from one infected donor to several recipients: a long-term follow-up. J Gen Virol 85, 441–450.[CrossRef]
    [Google Scholar]
  19. Malpica, J. M., Fraile, A., Moreno, I., Obies, C. I., Drake, J. W. & Garcia-Arenal, F. ( 2002; ). The rate and character of spontaneous mutations in an RNA virus. Genetics 162, 1505–1511.
    [Google Scholar]
  20. Nei, M. ( 1987; ). Molecular Evolutionary Genetics, pp. 190–191. New York, NY: Columbia University Press.
  21. Nei, M. & Gojobori, T. ( 1986; ). Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol 3, 418–423.
    [Google Scholar]
  22. Sawyer, S. ( 1989; ). Statistical tests for detecting gene conversion. Mol Biol Evol 6, 526–538.
    [Google Scholar]
  23. Shi, B. J., Habili, N., Gafny, R. & Symons, R. H. ( 2004; ). Extensive variation of sequence within isolates of grapevine virus B+. Virus Genes 29, 279–285.[CrossRef]
    [Google Scholar]
  24. Simmonds, P. ( 2004; ). Genetic diversity and evolution of hepatitis C virus – 15 years on. J Gen Virol 85, 3173–3188.[CrossRef]
    [Google Scholar]
  25. Simmonds, N. W. & Shepherd, K. ( 1955; ). Taxonomy and origins of cultivated bananas. J Linn Soc Bot 55, 302–312.[CrossRef]
    [Google Scholar]
  26. Stover, R. H. & Simmonds, N. W. ( 1987; ). Bananas, 3rd edn. New York, NY: Longman Scientific and Technical.
  27. Teycheney, P.-Y., Marais, A., Svanella-Dumas, L., Dulucq, M.-J. & Candresse, T. ( 2005; ). Molecular characterization of banana virus X (BVX), a novel member of the Flexiviridae family. Arch Virol 150, 1715–1727.[CrossRef]
    [Google Scholar]
  28. Thomas, J. E., Lockhart, B. & Iskra-Caruana, M.-L. ( 1999; ). Banana mild mosaic virus. In Diseases of Banana, Abaca and Enset, pp. 275–278. Edited by D. R. Jones. Wallingford, UK: CABI.
  29. 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 24, 4876–4882.
    [Google Scholar]
  30. Tuplin, A., Evans, D. J. & Simmonds, P. ( 2004; ). Detailed mapping of RNA secondary structures in core and NS5B-encoding region sequences of hepatitis C virus by RNase cleavage and novel bioinformatic prediction methods. J Gen Virol 85, 3037–3047.[CrossRef]
    [Google Scholar]
  31. Voinnet, O. ( 2005; ). Induction and suppression of RNA silencing: insights from viral infections. Nat Rev Genet 6, 206–220.[CrossRef]
    [Google Scholar]
  32. Waterhouse, P. M., Wang, M. B. & Lough, T. ( 2001; ). Gene silencing as an adaptive defence against viruses. Nature 411, 834–842.[CrossRef]
    [Google Scholar]
  33. Wetzel, T., Candresse, T., Macquaire, G., Ravelonandro, M. & Dunez, J. ( 1992; ). A highly sensitive immunocapture polymerase chain reaction method for plum pox potyvirus detection. J Virol Methods 39, 27–37.[CrossRef]
    [Google Scholar]
  34. Yoshikawa, N., Matsuda, H., Oda, Y., Isogai, M., Takahashi, T., Ito, T. & Yoshida, K. ( 2001; ). Genome heterogeneity of Apple stem pitting virus in apple trees. Acta Hortic 550, 285–290.
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/jgv/10.1099/vir.0.81197-0
Loading
/content/journal/jgv/10.1099/vir.0.81197-0
Loading

Data & Media loading...

Supplements

vol. , part 11, pp. 3179 - 3187

Name, genomic group and country of origin of banana accessions originating from the CIRAD collection in Guadeloupe used as source of .

Name, genomic group and country of origin of banana accessions originating from other sources used as source of . [Single PDF file](2763 KB)



PDF

Most cited articles

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