1887

Abstract

The gene sequence is more variable than that of the 16S rRNA gene. Comparative phylogenetic analyses with 16S rRNA and gene sequences from 80 and 83 phytoplasma strains, respectively, were performed to assess the efficacy of these sequences for delineating phytoplasma strains within each 16Sr group. The phylogenetic interrelatedness among phytoplasma taxa inferred by gene-based phylogeny was nearly congruent with that inferred by 16S rRNA gene-based phylogeny. Phylogenetic analysis based on the gene permitted finer differentiation of phytoplasma strains, however. The gene-based phylogeny not only readily resolved 16Sr subgroups within a given 16Sr group, but also delineated distinct lineages irresolvable by 16S rRNA gene-based phylogeny. Such high resolving power makes the gene a more useful genetic marker than the 16S rRNA gene for finer differentiation of closely related phytoplasma strains based on RFLP analysis with selected restriction enzymes. Such strains were readily identified by collective RFLP patterns. The genetic interrelationships among these strains were determined by pattern similarity coefficients, which coincided with delineations by phylogenetic analysis. This study also revealed two heterogeneous operons present in the phytoplasma clade. This latter finding may have significant implications for phytoplasma evolution.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.019695-0
2010-12-01
2024-04-25
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/60/12/2887.html?itemId=/content/journal/ijsem/10.1099/ijs.0.019695-0&mimeType=html&fmt=ahah

References

  1. Bertaccini A. 2007; Phytoplasmas: diversity, taxonomy, and epidemiology. Front Biosci 12:673–689 [CrossRef]
    [Google Scholar]
  2. Cai H., Wei W., Davis R. E., Chen H., Zhao Y. 2008; Genetic diversity among phytoplasmas infecting Opuntia species: virtual RFLP analysis identifies new subgroups in the peanut witches'-broom phytoplasma group. Int J Syst Evol Microbiol 58:1448–1457 [CrossRef]
    [Google Scholar]
  3. Green M. J., Thompson D. A., MacKenzie D. J. 1999; Easy and efficient DNA extraction from woody plants for the detection of phytoplasmas by polymerase chain reaction. Plant Dis 83:482–485 [CrossRef]
    [Google Scholar]
  4. 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]
  5. Hodgetts J., Boonham N., Mumford R., Harrison N., Dickinson M. 2008; Phytoplasma phylogenetics based on analysis of secA and 23S rRNA gene sequences for improved resolution of candidate species of ‘ Candidatus Phytoplasma’. Int J Syst Evol Microbiol 58:1826–1837 [CrossRef]
    [Google Scholar]
  6. Hogenhout S. A., Oshima K., Ammar E.-D., Kakizawa S., Kingdom H. N., Namba S. 2008; Phytoplasmas: bacteria that manipulate plants and insects. Mol Plant Pathol 9:403–423 [CrossRef]
    [Google Scholar]
  7. 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]
  8. 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]
  9. 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]
  10. 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]
  11. 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]
  12. Lee I.-M., Gundersen-Rindal D. E., Davis R. E., Bartoszyk I. M. 1998a; 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]
  13. Lee I.-M., Gundersen-Rindal D. E., Bertaccini A. 1998b; Phytoplasma: ecology and genomic diversity. Phytopathology 88:1359–1366 [CrossRef]
    [Google Scholar]
  14. Lee I.-M., Davis R. E., Gundersen-Rindal D. E. 2000; Phytoplasma: phytopathogenic mollicutes. Annu Rev Microbiol 54:221–255 [CrossRef]
    [Google Scholar]
  15. 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]
  16. Lee I.-M., Martini M., Marcone C., Zhu S. F. 2004a; Classification of phytoplasma strains in the elm yellows group (16SrV) and proposal of ‘ Candidatus Phytoplasma ulmi’ for the phytoplasma associated with elm yellows. Int J Syst Evol Microbiol 54:337–347 [CrossRef]
    [Google Scholar]
  17. Lee I.-M., Gundersen-Rindal 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]
  18. 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]
  19. 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]
  20. 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]
  21. 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]
  22. 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 Forest Pathol 27:45–54 [CrossRef]
    [Google Scholar]
  23. 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]
  24. Marcone C., Lee I.-M., Davis R. E., Ragozzino A., Seemüller E. 2000; Classification of aster yellows-group phytoplasmas based on combined analyses of rRNA and tuf gene sequences. Int J Syst Evol Microbiol 50:1703–1713
    [Google Scholar]
  25. 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]
  26. Martini M., Lee I.-M., Bottner K. D., Zhao Y., Botti S., Bertaccini A., Harrison N. A., Carraro L., Marcone C. other authors 2007; Ribosomal protein gene-based phylogeny for finer differentiation and classification of phytoplasmas. Int J Syst Evol Microbiol 57:2037–2051 [CrossRef]
    [Google Scholar]
  27. Murray R. G. E., Schleifer K. H. 1994; Taxonomic notes: a proposal for recording the properties of putative taxa of procaryotes. Int J Syst Bacteriol 44:174–176 [CrossRef]
    [Google Scholar]
  28. Razin S., Yogev D., Naot Y. 1998; Molecular biology and pathology of mycoplasmas. Microbiol Mol Biol Rev 62:1094–1156
    [Google Scholar]
  29. 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]
  30. 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]
  31. 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]
  32. 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]
  33. Suh J.-W., Boylan S. A., Oh S.-H., Price C. W. 1996; Genetic and transcriptional organization of the Bacillus subtilis spc - α region. Gene 169:17–23 [CrossRef]
    [Google Scholar]
  34. Swofford D. L. 1998 Phylogenetic analysis using parsimony (paup), version 4 Sunderland, MA: Sinauer Associates;
    [Google Scholar]
  35. Vandamme P., Pot B., Gillis M., De Vos P., Kersters K., Swings J. 1996; Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol Rev 60:407–438
    [Google Scholar]
  36. Wei W., Davis R. E., Lee I.-M., Zhao Y. 2007; Computer-simulated RFLP analysis of 16S rRNA genes: identification of ten new phytoplasma groups. Int J Syst Evol Microbiol 57:1855–1867 [CrossRef]
    [Google Scholar]
  37. Wei W., Lee I.-M., Davis R. E., Suo X., Zhao Y. 2008; Automated RFLP pattern comparison and similarity coefficient calculation for rapid delineation of new and distinct phytoplasma 16Sr subgroup lineages. Int J Syst Evol Microbiol 58:2368–2377 [CrossRef]
    [Google Scholar]
  38. Weisburg W. G., Tully J. G., Rose D. L., Petzel J. P., Oyaizu H., Yang D., Mandelco L., Sechrest J., Lawrence T. G. other authors 1989; A phylogenetic analysis of the mycoplasmas: basis for their classification. J Bacteriol 171:6455–6467
    [Google Scholar]
  39. Zhao Y., Wei W., Lee I.-M., Shao J., Suo X., Davis R. E. 2009; Construction of an interactive online phytoplasma classification tool, i PhyClassifier, and its application in analysis of the peach X-disease phytoplasma group (16SrIII. Int J Syst Evol Microbiol 59:2582–2593 [CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.019695-0
Loading
/content/journal/ijsem/10.1099/ijs.0.019695-0
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