Phylogenetic analysis of Xanthomonas species by comparison of partial gyrase B gene sequences

International Journal of Systematic and Evolutionary Microbiology

Volumn 57, Issue 12, 2007, Pages 2881-2887

  Parkinson, Neil ^a   Aritua, Valentine ^b   Heeney, John ^a   Cowie, Claire ^a   Bew, Janice ^a   Stead, David ^a  

^a CENTRAL SCIENCE LABORATORY   (United Kingdom)

^b Kawanda Agricultural Research Institute   (Uganda)

Author keywords

[No Author keywords available]

Indexed keywords

DNA TOPOISOMERASE (ATP HYDROLYSING) B;

ARTICLE; BACTERIAL GENE; BACTERIAL STRAIN; BACTERIUM IDENTIFICATION; BOOTSTRAPPING; DNA DNA HYBRIDIZATION; GENE SEQUENCE; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; SPECIES COMPARISON; XANTHOMONAS; XANTHOMONAS ALBILINEANS; XANTHOMONAS ALFALFA; XANTHOMONAS ARBORICOLA; XANTHOMONAS AXONOPODIS; XANTHOMONAS CAMPESTRIS; XANTHOMONAS CASSAVA; XANTHOMONAS CITRI; XANTHOMONAS CODIAEI; XANTHOMONAS CUCURBITA; XANTHOMONAS CYNARA; XANTHOMONAS FUSCANS; XANTHOMONAS GARDNERI; XANTHOMONAS HORTORUM; XANTHOMONAS HYCINTHI; XANTHOMONAS MELONIS; XANTHOMONAS ORYZA; XANTHOMONAS PERFORANS; XANTHOMONAS POPULI; XANTHOMONAS SACCHARI; XANTHOMONAS THEICOLA; XANTHOMONAS TRANSLUCENS; XANTHOMONAS VASICOLA; XANTHOMONAS VESICATORIA;

BACTERIAL PROTEINS; CLUSTER ANALYSIS; DNA GYRASE; DNA, BACTERIAL; MOLECULAR SEQUENCE DATA; PHYLOGENY; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, NUCLEIC ACID; XANTHOMONAS;

XANTHOMONAS; XANTHOMONAS ALBILINEANS; XANTHOMONAS ARBORICOLA; XANTHOMONAS AXONOPODIS; XANTHOMONAS CAMPESTRIS; XANTHOMONAS CASSAVAE; XANTHOMONAS CITRI; XANTHOMONAS CODIAEI; XANTHOMONAS CUCURBITAE; XANTHOMONAS CYNARAE; XANTHOMONAS GARDNERI; XANTHOMONAS HORTORUM; XANTHOMONAS HYACINTHI; XANTHOMONAS MELONIS; XANTHOMONAS ORYZAE; XANTHOMONAS POPULI; XANTHOMONAS SACCHARI; XANTHOMONAS THEICOLA; XANTHOMONAS TRANSLUCENS; XANTHOMONAS VASICOLA;

EID: 37449010217     PISSN: 14665026     EISSN: None     Source Type: Journal    
DOI: 10.1099/ijs.0.65220-0     Document Type: Article

References (33)

1. Ait Tayeb, L., Ageron, E., Grimont, F. & Grimont, P. (2005). Molecular phylogeny of the genus Pseudomonas based on rpoB sequences and application for identification of isolates. Res Microbiol 156, 763-773.
2. da Silva, A. C. R., Ferro, J. A., Reinach, F. C., Farah, C. S., Furlan, L., Quaggio, R., Monteiro-Vitorello, C., Van Sluys, M. M., Almeida, N. & other authors (2002). Comparison of the genomes of two Xanthomonas pathogens with differing host specificities. Nature 417, 459-463.
3. Euzéby, J. (2006). In Validation of the Publication of New Names and New Combinations Previously Effectively Published Outside the IJSB, List 109. Int J Syst Evol Microbiol 56, 925-927.
4. Euzéby, J. (2007). In List of New Names and New Combinations Previously Effectively, but not Validly, Published, List 115. Int J Syst Evol Microbiol 57, 893-897.
5. Fegan, M. & Prior, P. (2005). How complex is the "Ralstonia solanacearum species complex"? In Bacterial Wilt Disease and the Ralstonia solanacearum Complex, pp. 449-461. Edited by C. Allen, P. Prior & A. Hayward. Saint Paul, MN: American Phytopathological Society.
6. Gabriel, D. W., Kingsley, M. T., Hunter, J. E. & Gottwald, T. (1989). Reinstatement of Xanthomonas citri (ex Hasse) and X. phaseoli (ex Smith) to species and reclassification of all X. campestris pv. citri strains. Int J Syst Bacteriol 39, 14-22.
7. 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.
8. Hauben, L., Vauterin, L., Swings, J. & Moore, E. (1997). Comparison of 16S ribosomal DNA sequences of all Xanthomonas species. Int J Syst Bacteriol 47, 328-335.
9. Jones, J. B., Lacy, G. H., Bouzar, H., Stall, R. E. & Schaad, N. W. (2004). Reclassification of the xanthomonads associated with bacterial spot disease of tomato and pepper. Syst Appl Microbiol 27, 755-762.
10. Jukes, T. & Cantor, C. (1969). Evolution of protein molecules. In Mammalian Protein Metabolism, pp. 21-132. Edited by H.N. Munro. New York: Academic Press.
11. Lee, B. M., Park Y. J., Park, D. S., Kang, H. W., Kim, J. G., Song, E. S., Park, I. C., Yoon, U. H., Hahn, J. H. & other authors (2005). The genome sequence of Xanthomonas oryzae pathovar oryzae KACC10331, the bacterial blight pathogen of rice. Nucleic Acids Res 33, 577-586.
12. Louws, F. J., Fulbright D. W., Stephens, C. T. & De Bruijn, F. J. (1994). Specific genomic fingerprints of phytopathogenic Xanthomonas and Pseudomonas pathovars and strains, generated with repetitive sequences and PCR. Appl Environ Microbiol 60, 2286-2295.
13. Martin, B., Humbert, O., Camara, M., Guenzi, E., Walker, J., Mitchell, T., Andrew, P., Prudhomme, M., Alloing, G. & other authors (1992). A highly conserved repeated DNA element located in the chromosome of Streptococcus pneumoniae. Nucleic Acids Res 20, 3479-3483.
14. Paradis, S., Boissnot, M., Paquette, N., Bélanger, D., Martel, E., Boudreau, D., Picard, J., Ouellette, M., Roy, P. & Bergeron, M. (2005). Phylogeny of the Enterobacteriaceae based on encoding elongation factor Tu and F-ATPase β-subunit. Int J Syst Evol Microbiol 55, 2013-2025.
15. Poussier, S., Prior, P., Luisetti, J., Hayword, C. & Fegan, M. (2000). Partial sequencing of the hrpB and endoglucanase genes confirms and expands the known diversity within the Ralstonia solanacearum species complex. Syst Appl Microbiol 23, 479-486.
16. Rademaker, J. L. W., Louws, F. J., Schultz, M. H., Rossbach, U., Vauterin, L., Swings, J. & de Bruijn, F. J. (2005). A comprehensive species to strain taxonomic framework for Xanthomonas. Phytopathology 95, 1098-1111.
17. Saitou, N. & Nei, M. (1987). The neighbour-joining method: a new method of constructing phylogenetic trees. Mol Biol Evol 4, 406-425.
18. Sarkar, S. F. & Guttman, D. S. (2004). Evolution of the core genome of Pseudomonas syringae, a highly clonal endemic plant pathogen. Appl Environ Microbiol 70, 1999-2012.
19. Sarkar, S. F., Gordon, J. S., Martin, G. B. & Guttman, D. S. (2006). Comparative genomics of host-specific virulence in Pseudomonas syringae. Genetics 174, 1041-1056.
20. Schaad, N. W., Postnikova, E., Lacy, G. H., Sechler, A., Agarkova, I., Stromberg, P. E., Stromberg, V. K. & Vidaver, A. K. (2005). Reclassification of Xanthomonas campestris pv. citri (ex Hasse 1915) Dye 1978 forms A, B/C/D, and E as X. smithii subsp. citri (ex Hasse) sp. nov. nom. rev. comb. nov., X. fuscans subsp. aurantifolii (ex Gabriel 1989) sp. nov. nom. rev. comb. nov., and X. alfalfae subsp. citrumelo (ex Riker and Jones) Gabriel et al., 1989 sp. nov. nom. rev. comb. nov.; X. campestris pv. malvacearum (ex Smith 1901) Dye 1978 as X. smithii subsp. smithii nov. comb. nov. nom. nov.; X. campestris pv. alfalfae (ex Riker and Jones, 1935) Dye 1978 as X. alfalfae subsp. alfalfae (ex Riker et al., 1935) sp. nov. nom. rev.; and "var. fuscans" of X. campestris pv. phaseoli (ex Smith, 1987) Dye 1978 as X. fuscans subsp. fuscans sp. nov. Syst Appl Microbiol 28, 494-518.
21. Schaad, N. W., Postnikova, E., Lacy, G., Sechler, A., Agarkova, I., Stromberg, P. E., Stromberg, V. K. & Vidaver, A. K. (2006). (Erratum) Emended classification of xanthomonad pathogens on citrus. Syst Appl Microbiol 29, 690-695.
22. Schaad, N. W., Postnikova, E., Lacy, G., Sechler, A., Agarkova, I., Stromberg, P. E., Stromberg, V. K. & Vidaver, A. K. (2007). Xanthomonas alfalfae sp. nov., Xanthomonas citri sp. nov. and Xanthomonas fuscans sp. nov. In List of New Names and New Combinations Previously Effectively, but not Validly, Published, Validation List no. 115. Int J Syst Evol Microbiol 57, 893-897.
23. Stead, D. E. (1989). Grouping of Xanthomonas campestris pathovars of cereals and grasses by cellular fatty acid profiling. EPPO Bull 19, 51-68.
24. Stead, D. E. (1992). Grouping of plant-pathogenic and some other Pseudomonas spp. by using cellular fatty acid profiles. Int J Syst Bacteriol 42, 281-295.
25. Tajima, F. & Nei, M. (1984). Estimation of evolutionary distance between nucleotide sequences. Mol Biol Evol 1, 269-285.
26. Thieme, F., Koebnik, R., Bekel, T., Berger, C., Boch, J., Büttner, D., Caldana, C., Gaigalat, L., Goesmann, A. & other authors (2005). Insights into genome plasticity and pathogenicity of the plant pathogenic bacterium Xanthomonas campestris pv. vesicatoria revealed by the complete genome sequence. J Bacteriol 187, 7254-7266.
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.
28. Thwaites, R., Mansfield, J., Eden-Green, S. & Seal, S. (1999). RAPD and rep PCR-based fingerprinting of vascular bacterial pathogens of Musa spp. Plant Pathol 48, 121-128.
29. Trébaol, G., Gardan, C., Manceau, J., Tanguy, Y., Trilly, Y. & Boury, S. (2000). Genomic and phenotypic characterisation of Xanthomonas cynarae; a new species causing bacterial bract spot of artichoke (Cynara scolymus L.). Int J Syst Evol Microbiol 50, 1471-1478.
30. Van de Peer, Y. & De Wachter, R. (1993). TREECON: a software package for the construction and drawing of RT evolutionary trees. Comput Appl Biosci 9, 177-182.
31. Van den Mooter, M. & Swings, J. (1990). Numerical analysis of 295 phenotypic features of 266 Xanthomonas strains and related strains and an improved taxonomy of the genus. Int J Syst Bacteriol 40, 348-369.
32. Vauterin, L, Hoste, B., Kersters, K. & Swings, J. (1995). Reclassification of Xanthomonas. Int J Syst Bacteriol 45, 472-489.
33. Wichmann, G., Ritchie, D., Kousik, C. & Bergelson, J. (2005). Reduced genetic variation occurs among genes of the highly clonal plant pathogen Xanthomonas axonopodis pv. vesicatoria, including the effector gene avrBs2. Appl Environ Microbiol 71, 2418-2432.