1887

Abstract

Extensive phylogenetic analyses were performed based on sequences of the 16S rRNA gene and two ribosomal protein (rp) genes, () and (), from 46 phytoplasma strains representing 12 phytoplasma 16Sr groups, 16 other mollicutes and 28 Gram-positive walled bacteria. The phylogenetic tree inferred from rp genes had a similar overall topology to that inferred from the 16S rRNA gene. However, the rp gene-based tree gave a more defined phylogenetic interrelationship among mollicutes and Gram-positive walled bacteria. Both phylogenies indicated that mollicutes formed a monophyletic group. Phytoplasmas clustered with species and formed one clade paraphyletic with a clade consisting of the remaining mollicutes. The closest relatives of mollicutes were low-G+C-content Gram-positive bacteria. Comparative phylogenetic analyses using the 16S rRNA gene and rp genes were performed to evaluate their efficacy in resolving distinct phytoplasma strains. A phylogenetic tree was constructed based on analysis of rp gene sequences from 87 phytoplasma strains belonging to 12 16Sr phytoplasma groups. The phylogenetic relationships among phytoplasmas were generally in agreement with those obtained on the basis of the 16S rRNA gene in the present and previous works. However, the rp gene-based phylogeny allowed for finer resolution of distinct lineages within the phytoplasma 16Sr groups. RFLP analysis of rp gene sequences permitted finer differentiation of phytoplasma strains in a given 16Sr group. In this study, we also designed several semi-universal and 16Sr group-specific rp gene-based primers that allow for the amplification of 11 16Sr group phytoplasmas.

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2007-09-01
2024-03-28
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References

  1. Abou-Jawdah Y., Karakashian A., Sobh H., Martini M., Lee I.-M. 2002; An epidemic of almond witches'-broom in Lebanon: classification and phylogenetic relationships of the associated phytoplasma. Plant Dis 86:477–484 [CrossRef]
    [Google Scholar]
  2. Arocha Y., López M., Piñol B., Fernández M., Picornell B., Almeida R., Palenzuela I., Wilson M. R., Jones P. 2005; Candidatus Phytoplasma graminis’ and ‘ Candidatus Phytoplasma caricae’, two novel phytoplasmas associated with diseases of sugarcane, weeds and papaya in Cuba. Int J Syst Evol Microbiol 55:2451–2463 [CrossRef]
    [Google Scholar]
  3. Bai X., Zhang J., Ewing A., Miller S. A., Radek A. J., Shevchenko D. V., Tsukerman K., Walunas T., Lapidus A. other authors 2006; Living with genome instability: the adaptation of phytoplasmas to diverse environments of their insect and plant hosts. J Bacteriol 188:3682–3696 [CrossRef]
    [Google Scholar]
  4. Bertaccini A., Carraro L., Davies D., Laimer da Camara Machado M., Martini M., Paltrinieri S., Seemüller E. 2000; Micropropagation of a collection of phytoplasma strains in periwinkle and other host plants. In Proceedings of the 13th International Congress of the International Organization for Mycoplasmology Fukuoka, Japan: 14–19 July 2000p– 101
    [Google Scholar]
  5. Castresana J. 2000; Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 17:540–552 [CrossRef]
    [Google Scholar]
  6. Daubin V., Gouy M., Perriere G. 2002; A phylogenomic approach to bacterial phylogeny: evidence of a core of genes sharing a common history. Genome Res 12:1080–1090 [CrossRef]
    [Google Scholar]
  7. Gundersen D. E., Lee I.-M., Rehner S. A., Davis R. E., Kingsbury D. T. 1994; Phylogeny of mycoplasmalike organisms (phytoplasmas): a basis for their classification. J Bacteriol 176:5244–5254
    [Google Scholar]
  8. Gundersen D. E., Lee I.-M., Schaff D. A., Harrison N. A., Chang C. J., Davis R. E., Kinsbury D. T. 1996; Genomic diversity and differentiation among phytoplasma strains in 16S rRNA group I (aster yellows and related phytoplasmas) and III (X-disease and related phytoplasmas). Int J Syst Bacteriol 46:64–75 [CrossRef]
    [Google Scholar]
  9. IRPCM Phytoplasma/Spiroplasma Working Team – Phytoplasma Taxonomy Group; 2004; Candidatus Phytoplasma’, a taxon for the wall-less, non-helical prokaryotes that colonize plant phloem and insects. Int J Syst Evol Microbiol 54:1243–1255 [CrossRef]
    [Google Scholar]
  10. Jacobs K. A., Lee I.-M., Griffiths H. M., Miller F. D. Jr, Bottner K. D. 2003; A new member of the clover proliferation phytoplasmas group (16SrVI) associated with elm yellows in Illinois. Plant Dis 87:241–246 [CrossRef]
    [Google Scholar]
  11. Jung H. Y., Sawayanagi T., Kakizawa S., Nishigawa H., Miyata S., Oshima K., Ugaki M., Lee J. T., Hibi T., Namba S. 2002; Candidatus Phytoplasma castaneae’, a novel phytoplasma taxon associated with chestnut witches' broom disease. Int J Syst Evol Microbiol 52:1543–1549 [CrossRef]
    [Google Scholar]
  12. Lee I.-M., Davis R. E., Sinclair W. A., DeWitt N. D., Conti M. 1993a; Genetic relatedness of mycoplasmalike organisms detected in Ulmus spp. in the United States and Italy by means of DNA probes and polymerase chain reactions. Phytopathology 83:829–833 [CrossRef]
    [Google Scholar]
  13. Lee I.-M., Hammond R. W., Davis R. E., Gundersen D. E. 1993b; Universal amplification and analysis of pathogen 16S rDNA for classification and identification of mycoplasmalike organisms. Phytopathology 83:834–842 [CrossRef]
    [Google Scholar]
  14. Lee I.-M., Gundersen-Rindal D. E., Davis R. E., Bartoszyk I. M. 1998; Revised classification scheme of phytoplasmas based on RFLP analyses of 16S rRNA and ribosomal protein gene sequences. Int J Syst Bacteriol 48:1153–1169 [CrossRef]
    [Google Scholar]
  15. Lee I.-M., Davis R. E., Gundersen-Rindal D. E. 2000; Phytoplasma: phytopathogenic mollicutes. Annu Rev Microbiol 54:221–255 [CrossRef]
    [Google Scholar]
  16. Lee I.-M., Martini M., Bottner K. D., Dane R. A., Black M. C., Troxclair N. 2003; Ecological implications from a molecular analysis of phytoplasmas involved in an aster yellows epidemic in various crops in Texas. Phytopathology 93:1368–1377 [CrossRef]
    [Google Scholar]
  17. Lee I.-M., Martini M., Marcone C., Zhu S. F. 2004a; Classification of phytoplasma strains in the elm yellows group (16SrV) and proposition of ‘ Candidatus Phytoplasma ulmi’ for the phytoplasma associated with elm yellows. Int J Syst Evol Microbiol 54:337–347 [CrossRef]
    [Google Scholar]
  18. Lee I.-M., Gundersen D. E., Davis R. E., Bottner K. D., Marcone C., Seemüller E. 2004b; Candidatus Phytoplasma asteris’, a novel phytoplasma taxon associated with aster yellows and related diseases. Int J Syst Evol Microbiol 54:1037–1048 [CrossRef]
    [Google Scholar]
  19. Lee I.-M., Bottner K. D., Munyaneza J. E., Secor G. A., Gudmestad N. C. 2004c; Clover proliferation group (16SrVI) subgroup A (16SrVI-A) phytoplasma is a probable causal agent of potato purple top disease in Washington and Oregon. Plant Dis 88: 429
    [Google Scholar]
  20. Lee I.-M., Zhao Y., Bottner K. D. 2006a; SecY gene sequence analysis for finer differentiation of diverse strains in the aster yellows phytoplasma group. Mol Cell Probes 20:87–91 [CrossRef]
    [Google Scholar]
  21. Lee I.-M., Bottner K. D., Secor G., Rivera-Varas V. 2006b; Candidatus Phytoplasma americanum’, a phytoplasma associated with a potato purple top wilt disease complex. Int J Syst Evol Microbiol 56:1593–1597 [CrossRef]
    [Google Scholar]
  22. Lim P. O., Sears B. B. 1992; Evolutionary relationships of a plant-pathogenic mycoplasmalike organism and Acholeplasma laidlawii deduced from two ribosomal protein gene sequences. J Bacteriol 174:2606–2611
    [Google Scholar]
  23. Marcone C., Ragozzino A., Seemüller E. 1997a; Detection and identification of phytoplasmas in yellows-diseased weeds in Italy. Plant Pathol 46:530–537 [CrossRef]
    [Google Scholar]
  24. Marcone C., Ragozzino A., Seemüller E. 1997b; Identification and characterization of the phytoplasma associated with elm yellows in southern Italy and its relatedness to other phytoplasmas of the elm yellows group. Eur J For Pathol 27:45–54 [CrossRef]
    [Google Scholar]
  25. Marcone C., Ragozzino A., Seemüller E. 1997c; Detection and identification of phytoplasmas infecting vegetable, ornamental and forage crops in southern Italy. J Plant Pathol 79:211–217
    [Google Scholar]
  26. Martini M., Botti S., Marcone C., Marzachì C., Casati P., Bianco P. A., Benedetti R., Bertaccini A. 2002; Genetic variability among Flavescence dorée phytoplasmas from different origins in Italy and France. Mol Cell Probes 16:197–208 [CrossRef]
    [Google Scholar]
  27. Miyata S., Furuki K., Sawayanagi T., Oshima K., Kuboyama T., Tsuchizaki T., Ugaki M., Namba S. 2002a; Gene arrangement and sequence of str operon of phytoplasma resemble those of Bacillus more than those of Mycoplasma . J Gen Plant Pathol 68:62–67 [CrossRef]
    [Google Scholar]
  28. Miyata S., Furuki K., Oshima K., Sawayanagi T., Nishigawa H., Kakizawa S., Jung H., Ugaki M., Namba S. 2002b; Complete nucleotide sequence of the S10- spc operon of phytoplasma: gene organization and genetic code resemble those of Bacillus subtilis . DNA Cell Biol 21:527–534 [CrossRef]
    [Google Scholar]
  29. Montano H. G., Davis R. E., Dally E. L., Hogenhout S., Pimentel P., Brioso P. S. T. 2001; Candidatus Phytoplasma brasiliense’, a new phytoplasma taxon associated with hibiscus witches'-broom disease. Int J Syst Evol Microbiol 51:1109–1118 [CrossRef]
    [Google Scholar]
  30. Nei M., Kumar S. 2000 Molecular Evolution and Phylogenetics New York: Oxford University Press;
    [Google Scholar]
  31. Oshima K., Kakizawa S., Nishigawa H., Jung H., Wei W., Suzuki S., Arashida R., Nakata D., Miyata S. other authors 2004; Reductive evolution suggested from the complete genome sequence of a plant-pathogenic phytoplasma. Nat Genet 36:27–29 [CrossRef]
    [Google Scholar]
  32. Prince J. P., Davis R. E., Wolf T. K., Lee I.-M., Mogen B. D., Dally E. L., Bertaccini A., Credi R., Barba M. 1993; Molecular detection of diverse mycoplasmalike organisms (MLOs) associated with grapevine yellows and their classification with aster yellows, X-disease, and elm yellows MLOs. Phytopathology 83:1130–1137 [CrossRef]
    [Google Scholar]
  33. Razin S., Yogev D., Naot Y. 1998; Molecular biology and pathology of mycoplasmas. Microbiol Mol Biol Rev 62:1094–1156
    [Google Scholar]
  34. Schneider B., Seemüller E., Smart C. D., Kirkpatrick B. C. 1995; Phylogenetic classification of plant pathogenic mycoplasmalike organisms or phytoplasmas. In Molecular and Diagnostic Procedures in Mycoplasmology vol 1 pp 369–380 Edited by Razin R., Tully J. G. San Diego: Academic Press;
    [Google Scholar]
  35. Schneider B., Marcone C., Kampmann M., Ragozzino A., Lederer W., Cousin M. T., Seemüller E. 1997; Characterization and classification of phytoplasmas from wild and cultivated plants by RFLP and sequence analysis of ribosomal DNA. Eur J Plant Pathol 103:675–686 [CrossRef]
    [Google Scholar]
  36. Schneider B., Torres E., Martín M. P., Schröder M., Behnke H.-D., Seemüller E. 2005; Candidatus Phytoplasma pini’, a novel taxon from Pinus silvestris and Pinus halepensis . Int J Syst Evol Microbiol 55:303–307 [CrossRef]
    [Google Scholar]
  37. Seemüller E., Schneider B., Mäurer R., Ahrens U., Daire X., Kison H., Lorenz K. H., Firrao G., Avinent L. other authors 1994; Phylogenetic classification of phytopathogenic mollicutes by sequence analysis of 16S ribosomal DNA. Int J Syst Bacteriol 44:440–446 [CrossRef]
    [Google Scholar]
  38. Seemüller E., Marcone C., Lauer U., Ragozzino A., Göschl M. 1998; Current status of molecular classification of the phytoplasmas. J Plant Pathol 80:3–26
    [Google Scholar]
  39. Swofford D. L. 1998 paup*: phylogenetic analysis using parsimony (*and other methods), version 4 Sunderland, MA: Sinauer Associates;
    [Google Scholar]
  40. Valiunas D., Staniulis J., Davis R. E. 2006; Candidatus Phytoplasma fragariae’, a novel phytoplasma taxon discovered in yellows diseased strawberry, Fragaria  ×  ananassa . Int J Syst Evol Microbiol 56:277–281 [CrossRef]
    [Google Scholar]
  41. Wolf Y. I., Rogozin I. B., Grishin N. V., Tatusov R. L., Koonin E. V. 2001; Genome trees constructed using five different approaches suggest new major bacterial clades. BMC Evol Biol 1:8 [CrossRef]
    [Google Scholar]
  42. Zhao Y., Davis R. E., Lee I.-M. 2005; Phylogenetic positions of ‘ Candidatus Phytoplasma asteris’ and Spiroplasma kunkelii as inferred from multiple sets of concatenated core housekeeping proteins. Int J Syst Evol Microbiol 55:2131–2141 [CrossRef]
    [Google Scholar]
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