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Appl Environ Microbiol. Jul 1994; 60(7): 2286–2295.
PMCID: PMC201645

Specific genomic fingerprints of phytopathogenic Xanthomonas and Pseudomonas pathovars and strains generated with repetitive sequences and PCR.


DNA primers corresponding to conserved motifs in bacterial repetitive (REP, ERIC, and BOX) elements and PCR were used to show that REP-, ERIC-, and BOX-like DNA sequences are widely distributed in phytopathogenic Xanthomonas and Pseudomonas strains. REP-, ERIC, and BOX-PCR (collectively known as rep-PCR) were used to generate genomic fingerprints of a variety of Xanthomonas and Pseudomonas isolates and to identify pathovars and strains that were previously not distinguishable by other classification methods. Analogous rep-PCR-derived genomic fingerprints were generated from purified genomic DNA, colonies on agar plates, liquid cultures, and directly from lesions on infected plants. REP, ERIC, and BOX-PCR-generated fingerprints of specific Xanthomonas and Pseudomonas strains were found to yield similar conclusions wtih regard to the identity of and relationship between these strains. This suggests that the distribution of REP-, ERIC, and BOX-like sequences in these strains is a reflection of their genomic structure. Thus, the rep-PCR technique appears to be a rapid, simple, and reproducible method to identify and classify Xanthomonas and Pseudomonas strains, and it may be a useful diagnostic tool for these important plant pathogens.

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  • Achtman M, Pluschke G. Clonal analysis of descent and virulence among selected Escherichia coli. Annu Rev Microbiol. 1986;40:185–210. [PubMed]
  • Benedict AA, Alvarez AM, Pollard LW. Pathovar-Specific Antigens of Xanthomonas campestris pv. begoniae and X. campestris pv. pelargonii Detected with Monoclonal Antibodies. Appl Environ Microbiol. 1990 Feb;56(2):572–574. [PMC free article] [PubMed]
  • Berthier Y, Verdier V, Guesdon JL, Chevrier D, Denis JB, Decoux G, Lemattre M. Characterization of Xanthomonas campestris Pathovars by rRNA Gene Restriction Patterns. Appl Environ Microbiol. 1993 Mar;59(3):851–859. [PMC free article] [PubMed]
  • Cancilla MR, Powell IB, Hillier AJ, Davidson BE. Rapid genomic fingerprinting of Lactococcus lactis strains by arbitrarily primed polymerase chain reaction with 32P and fluorescent labels. Appl Environ Microbiol. 1992 May;58(5):1772–1775. [PMC free article] [PubMed]
  • de Bruijn FJ. Use of repetitive (repetitive extragenic palindromic and enterobacterial repetitive intergeneric consensus) sequences and the polymerase chain reaction to fingerprint the genomes of Rhizobium meliloti isolates and other soil bacteria. Appl Environ Microbiol. 1992 Jul;58(7):2180–2187. [PMC free article] [PubMed]
  • Denny TP, Gilmour MN, Selander RK. Genetic diversity and relationships of two pathovars of Pseudomonas syringae. J Gen Microbiol. 1988 Jul;134(7):1949–1960. [PubMed]
  • Fekete A, Bantle JA, Halling SM, Stich RW. Amplification fragment length polymorphism in Brucella strains by use of polymerase chain reaction with arbitrary primers. J Bacteriol. 1992 Dec;174(23):7778–7783. [PMC free article] [PubMed]
  • Frégeau CJ, Fourney RM. DNA typing with fluorescently tagged short tandem repeats: a sensitive and accurate approach to human identification. Biotechniques. 1993 Jul;15(1):100–119. [PubMed]
  • Gilson E, Clément JM, Brutlag D, Hofnung M. A family of dispersed repetitive extragenic palindromic DNA sequences in E. coli. EMBO J. 1984 Jun;3(6):1417–1421. [PMC free article] [PubMed]
  • Higgins CF, Ames GF, Barnes WM, Clement JM, Hofnung M. A novel intercistronic regulatory element of prokaryotic operons. Nature. 1982 Aug 19;298(5876):760–762. [PubMed]
  • Hulton CS, Higgins CF, Sharp PM. ERIC sequences: a novel family of repetitive elements in the genomes of Escherichia coli, Salmonella typhimurium and other enterobacteria. Mol Microbiol. 1991 Apr;5(4):825–834. [PubMed]
  • Jensen MA, Webster JA, Straus N. Rapid identification of bacteria on the basis of polymerase chain reaction-amplified ribosomal DNA spacer polymorphisms. Appl Environ Microbiol. 1993 Apr;59(4):945–952. [PMC free article] [PubMed]
  • Judd AK, Schneider M, Sadowsky MJ, de Bruijn FJ. Use of repetitive sequences and the polymerase chain reaction technique to classify genetically related Bradyrhizobium japonicum serocluster 123 strains. Appl Environ Microbiol. 1993 Jun;59(6):1702–1708. [PMC free article] [PubMed]
  • Kamoun S, Kado CI. A plant-inducible gene of Xanthomonas campestris pv. campestris encodes an exocellular component required for growth in the host and hypersensitivity on nonhosts. J Bacteriol. 1990 Sep;172(9):5165–5172. [PMC free article] [PubMed]
  • KING EO, WARD MK, RANEY DE. Two simple media for the demonstration of pyocyanin and fluorescin. J Lab Clin Med. 1954 Aug;44(2):301–307. [PubMed]
  • Krawiec S, Riley M. Organization of the bacterial chromosome. Microbiol Rev. 1990 Dec;54(4):502–539. [PMC free article] [PubMed]
  • Lupski JR, Weinstock GM. Short, interspersed repetitive DNA sequences in prokaryotic genomes. J Bacteriol. 1992 Jul;174(14):4525–4529. [PMC free article] [PubMed]
  • Martin B, Humbert O, Camara M, Guenzi E, Walker J, Mitchell T, Andrew P, Prudhomme M, Alloing G, Hakenbeck R, et al. A highly conserved repeated DNA element located in the chromosome of Streptococcus pneumoniae. Nucleic Acids Res. 1992 Jul 11;20(13):3479–3483. [PMC free article] [PubMed]
  • Sharples GJ, Lloyd RG. A novel repeated DNA sequence located in the intergenic regions of bacterial chromosomes. Nucleic Acids Res. 1990 Nov 25;18(22):6503–6508. [PMC free article] [PubMed]
  • Van den Mooter M, Swings J. Numerical analysis of 295 phenotypic features of 266 Xanthomonas strains and related strains and an improved taxonomy of the genus. Int J Syst Bacteriol. 1990 Oct;40(4):348–369. [PubMed]
  • Vera Cruz CM, Gosselé F, Kersters K, Segers P, Van den Mooter M, Swings J, De Ley J. Differentiation between Xanthomonas campestris pv. oryzae, Xanthomonas campestris pv. oryzicola and the bacterial 'brown blotch' pathogen on rice by numerical analysis of phenotypic features and protein gel electrophoregrams. J Gen Microbiol. 1984 Nov;130(11):2983–2999. [PubMed]
  • Versalovic J, Kapur V, Mason EO, Jr, Shah U, Koeuth T, Lupski JR, Musser JM. Penicillin-resistant Streptococcus pneumoniae strains recovered in Houston: identification and molecular characterization of multiple clones. J Infect Dis. 1993 Apr;167(4):850–856. [PubMed]
  • Versalovic J, Koeuth T, Lupski JR. Distribution of repetitive DNA sequences in eubacteria and application to fingerprinting of bacterial genomes. Nucleic Acids Res. 1991 Dec 25;19(24):6823–6831. [PMC free article] [PubMed]
  • Versalovic J, Woods CR, Jr, Georghiou PR, Hamill RJ, Lupski JR. DNA-based identification and epidemiologic typing of bacterial pathogens. Arch Pathol Lab Med. 1993 Nov;117(11):1088–1098. [PubMed]
  • Welsh J, McClelland M. Fingerprinting genomes using PCR with arbitrary primers. Nucleic Acids Res. 1990 Dec 25;18(24):7213–7218. [PMC free article] [PubMed]
  • Williams JG, Kubelik AR, Livak KJ, Rafalski JA, Tingey SV. DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res. 1990 Nov 25;18(22):6531–6535. [PMC free article] [PubMed]
  • Woods CR, Jr, Versalovic J, Koeuth T, Lupski JR. Analysis of relationships among isolates of Citrobacter diversus by using DNA fingerprints generated by repetitive sequence-based primers in the polymerase chain reaction. J Clin Microbiol. 1992 Nov;30(11):2921–2929. [PMC free article] [PubMed]
  • Woods CR, Versalovic J, Koeuth T, Lupski JR. Whole-cell repetitive element sequence-based polymerase chain reaction allows rapid assessment of clonal relationships of bacterial isolates. J Clin Microbiol. 1993 Jul;31(7):1927–1931. [PMC free article] [PubMed]

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