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. 1997 Feb;63(2):498–505. doi: 10.1128/aem.63.2.498-505.1997

Assessment of genetic diversity among strains of Pseudomonas syringae by PCR-restriction fragment length polymorphism analysis of rRNA operons with special emphasis on P. syringae pv. tomato.

C Manceau 1, A Horvais 1
PMCID: PMC168340  PMID: 9023928

Abstract

Phylogenetic relationships among 77 bacterial strains belonging to Pseudomonas syringae and Pseudomonas viridiflava species were assessed by analysis of the PCR-restriction fragment length polymorphism (RFLP) patterns of three DNA fragments corresponding to rrs and rrl genes and the internal transcribed spacer, ITS1. No difference among all strains in rrs and rrl genes was observed with 14 restriction enzymes, which confirms the close relationships existing between these two species. The nucleotidic sequence of the internal transcripted spacer (ITS1) between rrs and rrl for the P. syringae pv. syringae strain CFBP1392 was determined. Restriction maps of the PCR-amplified ITS1 region were prepared and compared for all 77 strains. Seventeen RFLP patterns, forming three main clusters, were distinguished. One contained all strains of P. syringae pv. tomato and of other pathovars which had been previously described as closely related by either pathogenicity studies or biochemical analyses. This cluster was equally far from P. viridiflava and from other P. syringae pathovars. These other pathovars of P. syringae formed a less coherent taxon.

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Selected References

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  1. Brosius J., Dull T. J., Noller H. F. Complete nucleotide sequence of a 23S ribosomal RNA gene from Escherichia coli. Proc Natl Acad Sci U S A. 1980 Jan;77(1):201–204. doi: 10.1073/pnas.77.1.201. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Denny T. P., Gilmour M. N., Selander R. K. Genetic diversity and relationships of two pathovars of Pseudomonas syringae. J Gen Microbiol. 1988 Jul;134(7):1949–1960. doi: 10.1099/00221287-134-7-1949. [DOI] [PubMed] [Google Scholar]
  3. Fitch W. M., Margoliash E. Construction of phylogenetic trees. Science. 1967 Jan 20;155(3760):279–284. doi: 10.1126/science.155.3760.279. [DOI] [PubMed] [Google Scholar]
  4. Gurtler V., Wilson V. A., Mayall B. C. Classification of medically important clostridia using restriction endonuclease site differences of PCR-amplified 16S rDNA. J Gen Microbiol. 1991 Nov;137(11):2673–2679. doi: 10.1099/00221287-137-11-2673. [DOI] [PubMed] [Google Scholar]
  5. Gutell R. R., Schnare M. N., Gray M. W. A compilation of large subunit (23S-like) ribosomal RNA sequences presented in a secondary structure format. Nucleic Acids Res. 1990 Apr 25;18 (Suppl):2319–2330. doi: 10.1093/nar/18.suppl.2319. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. KING E. O., WARD M. K., RANEY D. E. Two simple media for the demonstration of pyocyanin and fluorescin. J Lab Clin Med. 1954 Aug;44(2):301–307. [PubMed] [Google Scholar]
  7. Laguerre G., Allard M. R., Revoy F., Amarger N. Rapid Identification of Rhizobia by Restriction Fragment Length Polymorphism Analysis of PCR-Amplified 16S rRNA Genes. Appl Environ Microbiol. 1994 Jan;60(1):56–63. doi: 10.1128/aem.60.1.56-63.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Lelliott R. A., Billing E., Hayward A. C. A determinative scheme for the fluorescent plant pathogenic pseudomonads. J Appl Bacteriol. 1966 Dec;29(3):470–489. doi: 10.1111/j.1365-2672.1966.tb03499.x. [DOI] [PubMed] [Google Scholar]
  9. Navarro E., Simonet P., Normand P., Bardin R. Characterization of natural populations of Nitrobacter spp. using PCR/RFLP analysis of the ribosomal intergenic spacer. Arch Microbiol. 1992;157(2):107–115. doi: 10.1007/BF00245277. [DOI] [PubMed] [Google Scholar]
  10. Neefs J. M., Van de Peer Y., Hendriks L., De Wachter R. Compilation of small ribosomal subunit RNA sequences. Nucleic Acids Res. 1990 Apr 25;18 (Suppl):2237–2317. doi: 10.1093/nar/18.suppl.2237. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Nei M., Li W. H. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc Natl Acad Sci U S A. 1979 Oct;76(10):5269–5273. doi: 10.1073/pnas.76.10.5269. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Nei M., Stephens J. C., Saitou N. Methods for computing the standard errors of branching points in an evolutionary tree and their application to molecular data from humans and apes. Mol Biol Evol. 1985 Jan;2(1):66–85. doi: 10.1093/oxfordjournals.molbev.a040333. [DOI] [PubMed] [Google Scholar]
  13. Ochman H., Wilson A. C. Evolution in bacteria: evidence for a universal substitution rate in cellular genomes. J Mol Evol. 1987;26(1-2):74–86. doi: 10.1007/BF02111283. [DOI] [PubMed] [Google Scholar]
  14. Saitou N., Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987 Jul;4(4):406–425. doi: 10.1093/oxfordjournals.molbev.a040454. [DOI] [PubMed] [Google Scholar]
  15. Sanger F., Nicklen S., Coulson A. R. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463–5467. doi: 10.1073/pnas.74.12.5463. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Toschka H. Y., Höpfl P., Ludwig W., Schleifer K. H., Ulbrich N., Erdmann V. A. Complete nucleotide sequence of a 23S ribosomal RNA gene from Pseudomonas aeruginosa. Nucleic Acids Res. 1987 Sep 11;15(17):7182–7182. doi: 10.1093/nar/15.17.7182. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Vaneechoutte M., De Beenhouwer H., Claeys G., Verschraegen G., De Rouck A., Paepe N., Elaichouni A., Portaels F. Identification of Mycobacterium species by using amplified ribosomal DNA restriction analysis. J Clin Microbiol. 1993 Aug;31(8):2061–2065. doi: 10.1128/jcm.31.8.2061-2065.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Vaneechoutte M., Rossau R., De Vos P., Gillis M., Janssens D., Paepe N., De Rouck A., Fiers T., Claeys G., Kersters K. Rapid identification of bacteria of the Comamonadaceae with amplified ribosomal DNA-restriction analysis (ARDRA). FEMS Microbiol Lett. 1992 Jun 15;72(3):227–233. doi: 10.1111/j.1574-6968.1992.tb05102.x. [DOI] [PubMed] [Google Scholar]
  19. Woese C. R. Bacterial evolution. Microbiol Rev. 1987 Jun;51(2):221–271. doi: 10.1128/mr.51.2.221-271.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]

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