1887

Abstract

The genus currently comprises 27 species with validly published names that are important crop and horticultural pathogens. We have constructed a phylogram from alignment of gyrase B () sequences for all xanthomonad species, both to indicate inter-species relatedness and as an aid for rapid and accurate species-level identification. The phylogeny indicated a monophyletic group, with and as the most ancestral species. Three species, , and , formed an early-branching group. Three clades were supported by high bootstrap values: group 1 comprised , and ; group 2 comprised , , , , and ; group 3 contained the remaining species, within which two further clades, supported by a 100% bootstrap value, were identified. Group 3A comprised , , and , together with , and , whose names were recently validly published. Group 3B contained the monocot pathogens and . Two recently identified species, and , were poorly discriminated and were related closely to . Three species, , and , had identical sequences. Partial sequencing of a further five genes from these species found only minor sequence differences that confirmed their close relatedness. Although branch lengths between species varied, indicating different degrees of genetic distinctiveness, the majority (=21) were well-differentiated, indicating the utility of the method as an identification tool, and we now use this method for routine diagnosis of xanthomonad species.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.65220-0
2007-12-01
2024-03-28
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/57/12/2881.html?itemId=/content/journal/ijsem/10.1099/ijs.0.65220-0&mimeType=html&fmt=ahah

References

  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 [CrossRef]
    [Google Scholar]
  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 [CrossRef]
    [Google Scholar]
  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 [CrossRef]
    [Google Scholar]
  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 [CrossRef]
    [Google Scholar]
  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.
    [Google Scholar]
  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 [CrossRef]
    [Google Scholar]
  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
    [Google Scholar]
  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 [CrossRef]
    [Google Scholar]
  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 [CrossRef]
    [Google Scholar]
  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
    [Google Scholar]
  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 [CrossRef]
    [Google Scholar]
  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
    [Google Scholar]
  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 [CrossRef]
    [Google Scholar]
  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 [CrossRef]
    [Google Scholar]
  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 [CrossRef]
    [Google Scholar]
  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 [CrossRef]
    [Google Scholar]
  17. Saitou N., Nei M. 1987; The neighbour-joining method: a new method of constructing phylogenetic trees. Mol Biol Evol 4:406–425
    [Google Scholar]
  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 [CrossRef]
    [Google Scholar]
  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 [CrossRef]
    [Google Scholar]
  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 [CrossRef]
    [Google Scholar]
  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 [CrossRef]
    [Google Scholar]
  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 [CrossRef]
    [Google Scholar]
  23. Stead D. E. 1989; Grouping of Xanthomonas campestris pathovars of cereals and grasses by cellular fatty acid profiling. EPPO Bull 19:51–68 [CrossRef]
    [Google Scholar]
  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 [CrossRef]
    [Google Scholar]
  25. Tajima F., Nei M. 1984; Estimation of evolutionary distance between nucleotide sequences. Mol Biol Evol 1:269–285
    [Google Scholar]
  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 [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. 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 [CrossRef]
    [Google Scholar]
  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 [CrossRef]
    [Google Scholar]
  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
    [Google Scholar]
  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 [CrossRef]
    [Google Scholar]
  32. Vauterin L., Hoste B., Kersters K., Swings J. 1995; Reclassification of Xanthomonas . Int J Syst Bacteriol 45:472–489 [CrossRef]
    [Google Scholar]
  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 [CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.65220-0
Loading
/content/journal/ijsem/10.1099/ijs.0.65220-0
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Supplementary material 2

PDF
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error