1887

Journal of General Virology header logo

Volume 86, Issue 10

Phylogenetic analysis of isolates of collected worldwide Free

Abstract

A study of molecular diversity was carried out on 136 sugar beets infected with (BNYVV, ) collected worldwide. The nucleotide sequences of the RNA-2-encoded CP, RNA-3-encoded p25 and RNA-5-encoded p26 proteins were analysed. The resulting phylogenetic trees allowed BNYVV to be classified into groups that show correlations between the virus clusters and geographic origins. The selective constraints on these three sequences were measured by estimating the ratio between synonymous and non-synonymous substitution rates () with maximum-likelihood models. The results suggest that selective constraints are exerted differently on the proteins. CP was the most conserved, with mean values ranging from 0·12 to 0·15, while p26 was less constrained, with mean values ranging from 0·20 to 0·33. Selection was detected in three amino acid positions of p26, with values of about 5·0. The p25 sequences presented the highest mean values (0·36–1·10), with strong positive selection (=4·7–54·7) acting on 14 amino acids, and particularly on amino acid 68, where the value was the highest so far encountered in plant viruses.

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

Article metrics loading...

/content/journal/jgv/10.1099/vir.0.81167-0
2005-10-01
2024-04-18
Loading full text...

Full text loading...

/deliver/fulltext/jgv/86/10/2897.html?itemId=/content/journal/jgv/10.1099/vir.0.81167-0&mimeType=html&fmt=ahah

References

  1. Asher M. J. C., Chwarszczynska D. M., Leaman M. 2002; The evaluation of rhizomania resistant sugar beet for the UK. Ann Appl Biol 141:101–109 [CrossRef]
     [Google Scholar]
  2. Biancardi E., Lewellen R. T., Biaggi M. D., Erichsen A. W., Stevanato P. 2002; The origin of rhizomania resistance in sugarbeet. Euphytica 127:383–397 [CrossRef]
     [Google Scholar]
  3. Canova A. 1959; On the pathology of sugarbeet. Informatore Fitopatologico 9:390–396
     [Google Scholar]
  4. 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]
  5. Dietrich C., Maiss E. 2003; Fluorescent labelling reveals spatial separation of potyvirus populations in mixed infected Nicotiana benthamiana plants. J Gen Virol 84:2871–2876 [CrossRef]
     [Google Scholar]
  6. Drake J. W., Holland J. 1999; Mutation rates among RNA viruses. Proc Natl Acad Sci U S A 96:13910–13913 [CrossRef]
     [Google Scholar]
  7. Eigen M. 1993; Viral quasispecies. Sci Am 269:42–49
     [Google Scholar]
  8. Elena S. F. 2002; Restrictions to RNA virus adaptation: an experimental approach. Antonie Van Leeuwenhoek 81:135–142 [CrossRef]
     [Google Scholar]
  9. Fares M. A., Moya A., Escarmis C., Baranowski E., Domingo E., Barrio E. 2001; Evidence for positive selection in the capsid protein-coding region of the foot-and-mouth disease virus (FMDV) subjected to experimental passage regimens. Mol Biol Evol 18:10–21 [CrossRef]
     [Google Scholar]
  10. Felsenstein J. 1997; An alternating least squares approach to inferring phylogenies from pairwise distances. Syst Biol 46:101–111 [CrossRef]
     [Google Scholar]
  11. Felsenstein J. 2004 phylip, Phylogeny Inference Package version 3.6, 3.6 edn. Seattle: Department of Genome Sciences, University of Washington;
     [Google Scholar]
  12. French R., Stenger D. C. 2003; Evolution of wheat streak mosaic virus: dynamics of population growth within plants may explain limited variation. Annu Rev Phytopathol 41:199–214 [CrossRef]
     [Google Scholar]
  13. Garcia-Arenal F., Fraile A., Malpica J. M. 2003; Variation and evolution of plant virus populations. Int Microbiol 6:225–232 [CrossRef]
     [Google Scholar]
  14. Harju V. A., Mumford R. A., Bockley A., Boonham N., Clover G. R. G., Weekes R., Henry C. M. 2002; Occurence in the United Kingdom of beet necrotic yellow vein virus isolates which contain RNA 5. Plant Pathol 51:811 [CrossRef]
     [Google Scholar]
  15. Hauser S., Weber C., Vetter G., Stevens M., Beuve M., Lemaire O. 2000; Improved detection and differentiation of poleroviruses infecting beet or rape by multiplex RT-PCR. J Virol Methods 89:11–21 [CrossRef]
     [Google Scholar]
  16. Heijbroek W., Musters P. M. S., Schoone A. H. L. 1999; Variation in pathenogenicity and multiplication of Beet necrotic yellow vein virus (BNYVV) in relation to the resistance of sugarbeet cultivars. Eur J Plant Pathol 105:397–405 [CrossRef]
     [Google Scholar]
  17. Jupin I., Guilley H., Richards K. E., Jonard G. 1992; Two proteins encoded by beet necrotic yellow vein virus RNA 3 influence symptom phenotype on leaves. EMBO J 11:479–488
     [Google Scholar]
  18. Koenig R., Lennefors B. L. 2000; Molecular analyses of European A, B and P type sources of beet necrotic yellow vein virus and detection of the rare P type in Kazakhstan. Arch Virol 145:1561–1570 [CrossRef]
     [Google Scholar]
  19. Koenig R., Jarausch W., Li Y., Commandeur U., Burgermeister W., Gehrke M., Luddecke P. 1991; Effect of recombinant beet necrotic yellow vein virus with different RNA compositions on mechanically inoculated sugarbeets. J Gen Virol 72:2243–2246 [CrossRef]
     [Google Scholar]
  20. Koenig R., Luddecke P., Haeberle A. M. 1995; Detection of beet necrotic yellow vein virus strains, variants and mixed infections by examining single-strand conformation polymorphisms of immunocapture RT-PCR products. J Gen Virol 76:2051–2055 [CrossRef]
     [Google Scholar]
  21. Koenig R., Haeberle A. M., Commandeur U. 1997; Detection and characterization of a distinct type of beet necrotic yellow vein virus RNA 5 in a sugarbeet growing area in Europe. Arch Virol 142:1499–1504 [CrossRef]
     [Google Scholar]
  22. Kruse M., Koenig R., Hoffmann A., Kaufmann A., Commandeur U., Solovyev A. G., Savenkov I., Burgermeister W. 1994; Restriction fragment length polymorphism analysis of reverse transcription-PCR products reveals the existence of two major strain groups of beet necrotic yellow vein virus. J Gen Virol 75:1835–1842 [CrossRef]
     [Google Scholar]
  23. Lauber E., Guilley H., Tamada T., Richards K. E., Jonard G. 1998; Vascular movement of beet necrotic yellow vein virus in Beta macrocarpa is probably dependent on an RNA 3 sequence domain rather than a gene product. J Gen Virol 79:385–393
     [Google Scholar]
  24. Lennefors B. L., Lindsten K., Koenig R. 2000; First record of A and B type beet necrotic yellow vein virus in sugar beets in Sweden. Eur J Plant Pathol 106:199–201 [CrossRef]
     [Google Scholar]
  25. Li H., Roossinck M. J. 2004; Genetic bottlenecks reduce population variation in an experimental RNA virus population. J Virol 78:10582–10587 [CrossRef]
     [Google Scholar]
  26. Link D., Schmidlin L., Schirmer A., Klein E., Erhardt M., Geldreich A., Lemaire O., Gilmer D. 2005; Functional characterization of the beet necrotic yellow vein virus RNA-5-encoded p26 protein: evidence for structural pathogenicity determinants. J Gen Virol 86:2115–2125 [CrossRef]
     [Google Scholar]
  27. Liu H. Y., Sears J. L., Lewellen R. T. 2005; Occurence of resistance-breaking beet necrotic yellow vein virus of sugar beet. Plant Dis 89:464–468 [CrossRef]
     [Google Scholar]
  28. Meunier A., Schmit J. F., Stas A., Kutluk N., Bragard C. 2003; Multiplex reverse transcription-PCR for simultaneous detection of beet necrotic yellow vein virus , beet soilborne virus, and beet virus Q and their vector polymyxa betae KESKIN on sugar beet. Appl Environ Microbiol 69:2356–2360 [CrossRef]
     [Google Scholar]
  29. Miyanishi M., Kusume T., Saito M., Tamada T. 1999; Evidence for three groups of sequence variants of beet necrotic yellow vein virus RNA 5. Arch Virol 144:879–892 [CrossRef]
     [Google Scholar]
  30. Moury B. 2004; Differential selection of genes of Cucumber mosaic virus subgroups. Mol Biol Evol 21:1602–1611 [CrossRef]
     [Google Scholar]
  31. Moury B., Morel C., Johansen E., Guilbaud L., Souche S., Ayme V., Caranta C., Palloix A., Jacquemond M. 2004; Mutations in Potato virus Y genome-linked protein determine virulence toward recessive resistances in Capsicum annuum and Lycopersicon hirsutum . Mol Plant Microbe Interact 17:322–329 [CrossRef]
     [Google Scholar]
  32. 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]
  33. Ota T., Nei M. 1994; Variance and covariances of the numbers of synonymous and nonsynonymous substitutions per site. Mol Biol Evol 11:613–619
     [Google Scholar]
  34. Quillet L., Guilley H., Jonard G., Richards K. 1989; In vitro synthesis of biologically active beet necrotic yellow vein virus RNA. Virology 172:293–301 [CrossRef]
     [Google Scholar]
  35. Rush C. M. 2003; Ecology and epidemiology of benyviruses and plasmodiophorid vectors. Annu Rev Phytopathol 41:567–592 [CrossRef]
     [Google Scholar]
  36. Sacristan S., Malpica J. M., Fraile A., Garcia-Arenal F. 2003; Estimation of population bottlenecks during systemic movement of tobacco mosaic virus in tobacco plants. J Virol 77:9906–9911 [CrossRef]
     [Google Scholar]
  37. Saito M., Kiguchi T., Kusume T., Tamada T. 1996; Complete nucleotide sequence of the Japanese isolate S of beet necrotic yellow vein virus RNA and comparison with European isolates. Arch Virol 141:2163–2175 [CrossRef]
     [Google Scholar]
  38. Sanjuan R., Moya A., Elena S. F. 2004a; The contribution of epistasis to the architecture of fitness in an RNA virus. Proc Natl Acad Sci U S A 101:15376–15379 [CrossRef]
     [Google Scholar]
  39. Sanjuan R., Moya A., Elena S. F. 2004b; The distribution of fitness effects caused by single-nucleotide substitutions in an RNA virus. Proc Natl Acad Sci U S A 101:8396–8401 [CrossRef]
     [Google Scholar]
  40. Schmidlin L., Link D., Mutterer J., Guilley H., Gilmer D. 2005; Use of a Beet necrotic yellow vein virus RNA-5-derived replicon as a new tool for gene expression. J Gen Virol 86:463–467 [CrossRef]
     [Google Scholar]
  41. Scholten O. E., Bock T. S. M. D., Klein-Lankhorst R. M., Lange W. 1999; Inheritance of resistance to Beet necrotic yellow vein virus in Beta vulgaris conferred by a second gene for resistance. Theor Appl Genet 99:740–746 [CrossRef]
     [Google Scholar]
  42. Sohi H., Maleki M. 2004; Evidence for presence of types A and B of beet necrotic yellow vein virus (BNYVV) in Iran. Virus Genes 29:353–358 [CrossRef]
     [Google Scholar]
  43. Suarez M. B., Grondona I., Garcia-Benavides P., Monte E., Garcia-Acha I. 1999; Characterization of beet necrotic yellow vein furovirus from Spanish sugar beets. Int Microbiol 2:87–92
     [Google Scholar]
  44. Takeshita M., Shigemune N., Kikuhara K., Furuya N., Takanami Y. 2004; Spatial analysis for exclusive interactions between subgroups I and II of cucumber mosaic virus in cowpea. Virology 328:45–51 [CrossRef]
     [Google Scholar]
  45. Tamada T. 1999; Benyviruses. In Encyclopedia of Virology . , 2nd edn. pp  154–160 London: Academic Press;
  46. Tamada T., Baba T. 1973; Beet necrotic yellow vein virus from rhizomania-affected sugar beet in Japan. Ann Phytopathol Soc Japan 39:325–332 [CrossRef]
     [Google Scholar]
  47. Tamada T., Shirako Y., Abe H., Saito M., Kigushi T., Harada T. 1989; Production and pathogenicity of isolates of beet necrotic yellow vein virus with different numbers of RNA components. J Gen Virol 70:3399–3409 [CrossRef]
     [Google Scholar]
  48. Tamada T., Kusume T., Uchino H., Kigushi T., Saito M. 1996; Evidence that beet necrotic yellow vein virus RNA-5 is involved in symptom development of sugarbeet roots. In Proceedings of the 3rd Symposium of the International Working Group on Plant Viruses with Fungal Vectors American Society of Sugar Beet Technologists; Denver:49
     [Google Scholar]
  49. Tamada T., Uchino H., Kusume T., Saito M. 1999; RNA 3 deletion mutants of beet necrotic yellow vein virus do not cause rhizomania disease in sugar beets. Phytopathology 89:1000–1006 [CrossRef]
     [Google Scholar]
  50. 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]
  51. Valkonen J. P., Rajamaki M. L., Kekarainen T. 2002; Mapping of viral genomic regions important in cross-protection between strains of a potyvirus. Mol Plant Microbe Interact 15:683–692 [CrossRef]
     [Google Scholar]
  52. Vetter G., Hily J. M., Klein E., Schmidlin L., Haas M., Merkle T., Gilmer D. 2004; Nucleo-cytoplasmic shuttling of the beet necrotic yellow vein virus RNA-3-encoded p25 protein. J Gen Virol 85:2459–2469 [CrossRef]
     [Google Scholar]
  53. Woelk C. H., Pybus O. G., Jin L., Brown D. W., Holmes E. C. 2002; Increased positive selection pressure in persistent (SSPE) versus acute measles virus infections. J Gen Virol 83:1419–1430
     [Google Scholar]
  54. Yang Z. 1997; PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 13:555–556
     [Google Scholar]
  55. Yang Z. Bielawski 2000; Statistical methods for detecting molecular adaptation. Trends Ecol Evol 15:496–503 [CrossRef]
     [Google Scholar]
  56. Yang Z., Nielsen R., Goldman N., Krabbe Pedersen A.-M. 2000; Codon-substitution models for heterogeneous selection pressure at amino-acid sites. Genetics 155:431–449
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/jgv/10.1099/vir.0.81167-0
Loading
Phylogenetic analysis of isolates of Beet necrotic yellow vein virus collected worldwide
J. Gen. Virol. 86, 2897 (2005); https://doi.org/10.1099/vir.0.81167-0
/content/journal/jgv/10.1099/vir.0.81167-0
/content/journal/jgv/10.1099/vir.0.81167-0
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