1887

Abstract

The 16S rRNA gene sequences for 34 strains, including 11 isolates, were determined to classify scab-causing spp. and relatives isolated from potato scab lesions collected in Jeju, Korea. The 16S–23S rDNA internally transcribed spacer (ITS) sequences were determined to investigate whether the 16S–23S ITS region is useful for analysing intra- and interspecific relationships in these bacteria. On the basis of phylogenetic analysis of 16S rRNA gene sequences, most of the isolates were classified as and . Isolate KJO61 was placed in an ambiguous taxonomic position between and . 16S–23S ITS region sequence analysis showed that tRNA genes were not found in this region of spp. The 16S–23S ITS regions of spp. exhibited various lengths and highly variable sequence similarities (35–100 %) within strains as well as intra- and interspecies. It was revealed that could be clearly differentiated from . However, it was clarified that ITS regions are not useful in phylogenetic analysis of spp.

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2004-01-01
2020-01-21
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References

  1. Bouchek-Mechiche, K., Gardan, L., Normand, P. & Jouan, B. ( 2000; ). DNA relatedness among strains of Streptomyces pathogenic to potato in France: description of three new species, S. europaeiscabiei sp. nov. and S. stelliscabiei sp. nov. associated with common scab, and S. reticuliscabiei sp. nov. associated with netted scab. Int J Syst Evol Microbiol 50, 91–99.[CrossRef]
    [Google Scholar]
  2. Chun, J. & Goodfellow, M. ( 1995; ). A phylogenetic analysis of the genus Nocardia with 16S rRNA gene sequences. Int J Syst Bacteriol 45, 240–245.[CrossRef]
    [Google Scholar]
  3. Conrads, G., Claros, M. C., Citron, D. M., Tyrrell, K. L., Merriam, V. & Goldstein, E. J. C. ( 2002; ). 16S–23S internal transcribed spacer sequences for analysis of the phylogenetic relationships among species of the genus Fusobacterium. Int J Syst Evol Microbiol 52, 493–499.
    [Google Scholar]
  4. Faucher, E., Paradis, E., Goyer, C., Hodge, N. C., Hogue, R., Stall, R. E. & Beaulieu, C. ( 1995; ). Characterization of streptomycetes causing deep-pitted scab of potato in Quebec, Canada. Int J Syst Bacteriol 45, 222–225.[CrossRef]
    [Google Scholar]
  5. García-Martínez, J., Bescós, I., Rodríguez-Sala, J. J. & Rodríguez-Valera, F. ( 2001; ). RISSC: a novel database for ribosomal 16S–23S RNA genes spacer regions. Nucleic Acids Res 29, 178–180.[CrossRef]
    [Google Scholar]
  6. Gonçalves, E. R. & Rosato, Y. B. ( 2002; ). Phylogenetic analysis of Xanthomonas species based upon 16S–23S rDNA intergenic spacer sequences. Int J Syst Evol Microbiol 52, 355–361.
    [Google Scholar]
  7. Goyer, C. & Beaulieu, C. ( 1997; ). Host range of streptomycete strains causing common scab. Plant Dis 81, 901–904.[CrossRef]
    [Google Scholar]
  8. Goyer, C., Faucher, E. & Beaulieu, C. ( 1996; ). Streptomyces caviscabies sp. nov., from deep-pitted lesions in potatoes in Quebec, Canada. Int J Syst Bacteriol 46, 635–639.[CrossRef]
    [Google Scholar]
  9. Gürtler, V. & Stanisich, V. A. ( 1996; ). New approaches to typing and identification of bacteria using the 16S–23S rDNA spacer region. Microbiology 142, 3–16.[CrossRef]
    [Google Scholar]
  10. Hain, T., Ward-Rainey, N., Kroppenstedt, R. M., Stackebrandt, E. & Rainey, F. A. ( 1997; ). Discrimination of Streptomyces albidoflavus strains based on the size and number of 16S–23S ribosomal DNA intergenic spacers. Int J Syst Bacteriol 47, 202–206.[CrossRef]
    [Google Scholar]
  11. Healy, F. G. & Lambert, D. H. ( 1991; ). Relationships among Streptomyces spp. causing potato scab. Int J Syst Bacteriol 41, 479–482.[CrossRef]
    [Google Scholar]
  12. Jukes, T. H. & Cantor, C. R. ( 1969; ). Evolution of protein molecules. In Mammalian Protein Metabolism, pp. 21–132. Edited by H. N. Munro. New York: Academic Press.
  13. Kreuze, J. F., Suomalainen, S., Paulin, L. & Valkonen, J. P. T. ( 1999; ). Phylogenetic analysis of 16S rRNA genes and PCR analysis of the nec1 gene from Streptomyces spp. causing common scab, pitted scab, and netted scab in Finland. Phytopathology 89, 462–469.[CrossRef]
    [Google Scholar]
  14. Kumar, S., Tamura, K., Jakobsen, I. B. & Nei, M. ( 2001; ). mega2: molecular evolutionary genetics analysis software. Bioinformatics 17, 1244–1245.[CrossRef]
    [Google Scholar]
  15. Labeda, D. P. & Lyons, A. J. ( 1992; ). DNA relatedness among strains of the sweet potato pathogen Streptomyces ipomoea (Person and Martin 1940) Waksman and Henrici 1948. Appl Environ Microbiol 58, 532–535.
    [Google Scholar]
  16. Lambert, D. H. & Loria, R. ( 1989a; ). Streptomyces scabies sp. nov., nom. rev. Int J Syst Bacteriol 39, 387–392.[CrossRef]
    [Google Scholar]
  17. Lambert, D. H. & Loria, R. ( 1989b; ). Streptomyces acidiscabies sp. nov. Int J Syst Bacteriol 39, 393–396.[CrossRef]
    [Google Scholar]
  18. Loria, R., Bukhalid, R. A., Fry, B. A. & King, R. R. ( 1997; ). Plant pathogenicity in the genus Streptomyces. Plant Dis 81, 836–846.[CrossRef]
    [Google Scholar]
  19. Mehling, A., Wehmeier, U. F. & Piepersberg, W. ( 1995; ). Nucleotide sequences of streptomycete 16S ribosomal DNA: towards a specific identification system for streptomycetes using PCR. Microbiology 141, 2139–2147.[CrossRef]
    [Google Scholar]
  20. Miyajima, K., Tanaka, F., Takeuchi, T. & Kuninage, S. ( 1998; ). Streptomyces turgidiscabies sp. nov. Int J Syst Bacteriol 48, 495–502.[CrossRef]
    [Google Scholar]
  21. Paradis, E., Goyer, C., Hodge, N. C., Hogue, R., Stall, R. E. & Beaulieu, C. ( 1994; ). Fatty acid and protein profiles of Streptomyces scabies strains isolated in eastern Canada. Int J Syst Bacteriol 44, 561–564.[CrossRef]
    [Google Scholar]
  22. Pospiech, A. & Neumann, B. ( 1995; ). A versatile quick-prep of genomic DNA from Gram-positive bacteria. Trends Genet 11, 217–218.[CrossRef]
    [Google Scholar]
  23. Saitou, N. & Nei, M. ( 1987; ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–425.
    [Google Scholar]
  24. Song, J., Weon, H.-Y., Yoon, S.-H., Park, D.-S., Goa, S.-J. & Suh, J.-W. ( 2001; ). Phylogenetic diversity of thermophilic actinomycetes and Thermoactinomyces spp. isolated from mushroom composts in Korea based on 16S rRNA gene sequences analysis. FEMS Microbiol Lett 202, 97–102.[CrossRef]
    [Google Scholar]
  25. Stackebrandt, E., Rainey, F. A. & Ward-Rainey, N. L. ( 1997; ). Proposal for a new hierarchic classification system, Actinobacteria classis nov. Int J Syst Bacteriol 47, 479–491.[CrossRef]
    [Google Scholar]
  26. Takeuchi, T., Sawada, H., Tanaka, F. & Matsuda, I. ( 1996; ). Phylogenetic analysis of Streptomyces spp. causing potato scab based on 16S rRNA sequences. Int J Syst Bacteriol 46, 476–479.[CrossRef]
    [Google Scholar]
  27. Thompson, J. D., Higgins, D. G. & Gibson, T. J. ( 1994; ). clustal w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22, 4673–4680.[CrossRef]
    [Google Scholar]
  28. Trüper, H. G. & Clari, L. D. ( 1997; ). Taxonomic note: necessary correction of specific epithets formed as substantives (nouns) ‘in apposition’. Int J Syst Bacteriol 47, 908–909.[CrossRef]
    [Google Scholar]
  29. Weisburg, W. G., Barns, S. M., Pelletier, D. A. & Lane, D. J. ( 1991; ). 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173, 697–703.
    [Google Scholar]
  30. Williams, S. T., Goodfellow, M., Alderson, G., Wellington, E. M. H., Sneath, P. H. A. & Sakin, M. J. ( 1983; ). Numerical classification of Streptomyces and related genera. J Gen Microbiol 129, 1743–1813.
    [Google Scholar]
  31. Woese, C. R. ( 1987; ). Bacterial evolution. Microbiol Rev 51, 221–271.
    [Google Scholar]
  32. Yoon, H. J., Lee, S. T. & Park, Y. H. ( 1998; ). Genetic analyses of the genus Nocardioides and related taxa based on 16S–23S rDNA internally transcribed spacer sequences. Int J Syst Bacteriol 48, 641–650.[CrossRef]
    [Google Scholar]
  33. Zhang, Z., Kudo, T., Nakajima, Y. & Wang, Y. ( 2001; ). Clarification of the relationship between the members of the family Thermomonosporaceae on the basis of 16S rDNA, 16S–23S rRNA internal transcribed spacer and 23S rDNA sequences and chemotaxonomic analyses. Int J Syst Evol Microbiol 51, 373–383.
    [Google Scholar]
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vol. , part 1, pp. 203-209

A neighbour-joining tree of isolates and spp. related to potato scab disease on the basis of 16S-23S ITS rDNA sequence is available as a PDF file. Some sequences were obtained from GenBank. The numbers at the branching points are the percentages of occurrence in 1000 bootstrapped trees. The bar indicates a distance of 0.05 substitutions per site.



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