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Volume 146, Issue 10

Phylogeny of the genus : intrageneric structure reconstructed from the nucleotide sequences of and genes

The GenBank accession numbers for the sequences determined in this work are: , D37926, D37297, D86005–D86019 and AB039381–AB039492; , D86020–D86036 and AB039493–AB039624.

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Abstract

Phylogenetic analysis of the genus was conducted by using the combined and nucleotide sequences of 31 validly described species of (a total of 125 strains). strains diverged into two major clusters designated intrageneric cluster I (IGC I) and intrageneric cluster II (IGC II). IGC I was further split into two subclusters, the ‘ complex’, which included , , , , and , and the ‘ complex’, which included and . IGC II was further split into three subclusters that were designated the ‘ complex’, the ‘ complex’ and the ‘ complex’. The ‘ complex’ included and . The ‘ complex’ was the cluster of phytopathogens including , , , , . and the pathovars of and . The ‘ complex’ was further divided into two subpopulations, the ‘ lineage’ and the ‘ lineage’. The ‘ lineage’ contained biotypes A, B and C, , pathovars, , and , while the ‘ lineage’ included , , , , biotypes B and G and biovar B. The strains of biotypes formed a polyphyletic group within the ‘ complex’.

  • Received:
  • Accepted:
  • Revised:
  • Published Online:
Keyword(s): gyrB , IGC, intrageneric cluster , NJ, neighbour-joining , PCR , phylogeny , Pseudomonas , rpoD and UPGMA, unweighted pair group method with arithmetic averages
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2000-10-01
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References

  1. Barnsley E. A. 1976; Role and regulation of the ortho and meta pathways of catechol metabolism in pseudomonads metabolizing naphthalene and salicylate. J Bacteriol 125:404–408
     [Google Scholar]
  2. Bennasar A., Guasp J., Lalucat J. 1998; Molecular methods for the detection and identification of Pseudomonas stutzeri in pure culture and environmental samples. Microb Ecol 35:22–53 [CrossRef]
     [Google Scholar]
  3. Brenner D. J., Mcwhorter A. C., Leete Kundson J. K., Steigerwalt A. G. 1982; Escherichia vulneris: a new species of Enterobacteriaceae associated with human wounds. J Clin Microbiol 15:1133–1140
     [Google Scholar]
  4. Cournoyer B., Sharp J. D., Astuto A., Gibbon M. J., Taylor J. D., Vivian A. 1995; Molecular characterization of the Pseudomonas syringae pv. pisi plasmid-borne avirulence gene avrPpiB which matches the R3 resistance locus in pea. Mol Plant–Microbe Interact 8:700–708 [CrossRef]
     [Google Scholar]
  5. Dixon M. T., Hillis D. M. 1993; Ribosomal RNA secondary structure: compensatory mutations and implications for phylogenetic analysis. Mol Biol Evol 10:256–267
     [Google Scholar]
  6. Felsenstein J. 1989; phylip – phylogeny inference package (version 3.2). Cladistics 5:164–166
     [Google Scholar]
  7. Fitch W. M. 1971; Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20:406–416 [CrossRef]
     [Google Scholar]
  8. Fox G. E., Wisotzkey J. D., Jurtshuk P. J. 1992; How close is close: 16S rRNA sequence identity may not be sufficient to guarantee species identity. Int J Syst Bacteriol 42:166–170 [CrossRef]
     [Google Scholar]
  9. Furukawa K., Hayase N., Taira K., Tomizuka N. 1989; Molecular relationship of chromosomal genes encoding biphenyl/polychlorinated biphenyl catabolism: some soil bacteria possess a highly conserved bph operon. J Bacteriol 171:5467–5472
     [Google Scholar]
  10. Gardan L., Bollet C., Abu Ghorrah M., Grimont F., Grimont A. D. 1992; DNA relatedness among the pathovar strains of Pseudomonas syringae subsp. savastanoi Janse (1982) and proposal of Pseudomonas savastanoi sp. nov. Int J Syst Bacteriol 42:606–612 [CrossRef]
     [Google Scholar]
  11. Hancock J. M., Tautz D., Dover G. A. 1988; Evolution of the secondary structures and compensatory mutations of the ribosomal RNAs of Drosophila melanogaster. Mol Biol Evol 5:393–414
     [Google Scholar]
  12. Jackson R. W., Athanassopoulos E., Tsiamis G.7 other authors 1999; Identification of a pathogenicity island, which contains genes for virulence and avirulence, on a large native plasmid in Pseudomonas syringae pathovar phaseolicola. Proc Natl Acad Sci U S A 96:10875–10880 [CrossRef]
     [Google Scholar]
  13. Kersters K., Ludwig W., Vancanneyt M., De Vos P., Gillis M., Schleifer K.-H. 1996; Recent changes in the classification of the pseudomonads; an overview. Syst Appl Microbiol 19:465–477 [CrossRef]
     [Google Scholar]
  14. Kimura M. 1980; A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120 [CrossRef]
     [Google Scholar]
  15. Laguerre G., Rigottier-Gois L., Lemanceau P. 1994; Fluorescent Pseudomonas species categorized by using polymerase chain reaction (PCR)/restriction fragment analysis of 16S rDNA. Mol Ecol 3:479–487 [CrossRef]
     [Google Scholar]
  16. Lonetto M., Gribskov M., Gross C. A. 1992; The sigma 70 family: sequence conservation and evolutionary relationships. J Bacteriol 174:3843–3849
     [Google Scholar]
  17. Moore E. R. B., Mau M., Arnscheidt A., Böttger E. C., Hutson R. A., Collins M. D., Van de Peer Y., De Wachter R., Timmis K. N. 1996; The determination and comparison of the 16S rRNA gene sequence of species of the genus Pseudomonas (sensu stricto) and estimation of the natural intrageneric relationships. Syst Appl Microbiol 19:478–492 [CrossRef]
     [Google Scholar]
  18. Palleroni N. J. 1984; Genus I. Pseudomonas Migula 1894, 237AL. In Bergey’s Manual of Systematic Bacteriology pp. 141–199Edited by Krieg N. J., Holt J. G. Baltimore: Wiliams & Wilkins;
     [Google Scholar]
  19. Rousset F., Pelandakis M., Solignac M. 1991; Evolution of compensatory substitutions through G.U intermediate state in Drosophila rRNA. Proc Natl Acad Sci U S A 88:10032–10036 [CrossRef]
     [Google Scholar]
  20. Saitou N., Nei M. 1987; The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425
     [Google Scholar]
  21. Shimao M., Nakamura T., Okuda A., Abe M., Harayama S. 1996; Characterization of transposon insertion mutants of mandelic acid-utilizing Pseudomonas putida strain A10L. Biosci Biotechnol Biochem 60:1051–1055 [CrossRef]
     [Google Scholar]
  22. Sokal R. R., Michener C. D. 1958; A statistical method for evaluating systematic relationships. Univ Kans Sci Bull 28:1409–1438
     [Google Scholar]
  23. Stackebrandt E., Goebel B. 1994; Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 44:846–849 [CrossRef]
     [Google Scholar]
  24. Stanier R. Y., Palleroni N. J., Doudoroff M. 1966; The aerobic pseudomonads: a taxonomic study. J Gen Microbiol 43:159–271 [CrossRef]
     [Google Scholar]
  25. Takeo M., Maeda Y., Okada H., Miyama K., Mori K., Ike M., Fujita M. 1995; Molecular cloning and sequencing of the phenol hydroxylase gene from Pseudomonas putida BH. J Ferment Bioeng 79:485–488 [CrossRef]
     [Google Scholar]
  26. 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]
  27. Verhille S., Baida N., Dabboussi F., Izard D., Leclerc H. 1999; Taxonomic study of bacteria isolated from natural mineral waters: proposal of Pseudomonas jessenii sp. nov. and Pseudomonas mandelii sp. nov. Syst Appl Microbiol 22:45–58 [CrossRef]
     [Google Scholar]
  28. Watt P. M., Hickson I. D. 1994; Structure and function of type II DNA topoisomerases. Biochem J 303:681–695
     [Google Scholar]
  29. Wayne L. G., Brenner D. J., Colwell R. R.9 other authors 1987; International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463–464 [CrossRef]
     [Google Scholar]
  30. Yamamoto S., Harayama S. 1995; PCR amplification and direct sequencing of gyrB genes with universal primers and their application to the detection and taxonomic analysis of Pseudomonas putida strains. Appl Environ Microbiol 61:1104–1109
     [Google Scholar]
  31. Yamamoto S., Harayama S. 1996; Phylogenetic analysis of Acinetobacter strains based on the nucleotide sequences of gyrB genes and on the amino acid sequences of their products. . Int J Syst Bacteriol 46:506–511 [CrossRef]
     [Google Scholar]
  32. Yamamoto S., Harayama S. 1998; Phylogenetic relationships of Pseudomonas putida strains deduced from the nucleotide sequences of gyrB, rpoD and 16S rRNA genes. Int J Syst Bacteriol 48:813–819 [CrossRef]
     [Google Scholar]
  33. Yamamoto S., Bouvet P. J. M., Harayama S. 1999; Phylogenetic structures of the genus Acinetobacter based on gyrB sequences: comparison with the grouping by DNA-DNA hybridization. Int J Syst Bacteriol 49:87–95 [CrossRef]
     [Google Scholar]
  34. Yen K. M., Gunsalus I. C. 1985; Regulation of naphthalene catabolic genes of plasmid NAH7. J Bacteriol 162:1008–1013
     [Google Scholar]
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Phylogeny of the genus Pseudomonas: intrageneric structure reconstructed from the nucleotide sequences of gyrB and rpoD genesThe GenBank accession numbers for the sequences determined in this work are: gyrB, D37926, D37297, D86005–D86019 and AB039381–AB039492; rpoD, D86020–D86036 and AB039493–AB039624.
Microbiology 146, 2385 (2000); https://doi.org/10.1099/00221287-146-10-2385
/content/journal/micro/10.1099/00221287-146-10-2385
/content/journal/micro/10.1099/00221287-146-10-2385
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