1887

Abstract

We have used amplified fragment length polymorphism (AFLP), multilocus sequence analysis (MLSA) and DNA–DNA hybridization for genotypic classification of pathovars associated with the plant family Anacardiaceae. AFLP and MLSA results showed congruent phylogenetic relationships of the pathovar (responsible for mango bacterial canker) with strains of subgroup 9.5. This subgroup includes pv. (synonym ). Similarly, the pathovar , which causes cashew bacterial spot in Brazil, was included in subgroup 9.6 (synonym ). Based on the thermal stability of DNA reassociation, consistent with the AFLP and MLSA data, the two pathovars share a level of similarity consistent with their being members of the same species. The recent proposal to elevate pv. to species level as is supported by our data. Therefore, the causal agents of mango bacterial canker and cashew bacterial spot should be classified as pathovars of , namely pv. (pathotype strain CFBP 1716) and pv. (pathotype strain CFBP 2913), respectively. should be considered to be a later heterotypic synonym of .

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2009-02-01
2019-08-22
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References

  1. Aabenhus, R., On, S. L. W., Siemer, B. L., Permin, H. & Andersen, L. P. ( 2005; ). Delineation of Campylobacter concisus genomospecies by amplified fragment length polymorphism analysis and correlation of results with clinical data. J Clin Microbiol 43, 5091–5096.[CrossRef]
    [Google Scholar]
  2. Ah-You, N., Gagnevin, L., Chiroleu, F., Jouen, E., Neto, J. R. & Pruvost, O. ( 2007; ). Pathological variations within Xanthomonas campestris pv. mangiferaeindicae support its separation into three distinct pathovars that can be distinguished by amplified fragment length polymorphism. Phytopathology 97, 1568–1577.[CrossRef]
    [Google Scholar]
  3. Ausubel, F. M., Brent, R., Kingston, R. E., Moore, D. D., Seidman, J. G., Smith, J. A. & Struhl, K. ( 1991; ). Current Protocols in Molecular Biology. New York: Wiley.
  4. Boudon, S., Manceau, C. & Notteghem, J. L. ( 2005; ). Structure and origin of Xanthomonas arboricola pv. pruni populations causing bacterial spot of stone fruit trees in Western Europe. Phytopathology 95, 1081–1088.[CrossRef]
    [Google Scholar]
  5. Brenner, D. J., McWhorter, A. C., Leete-Knutson, 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]
  6. Chelo, I. M., Zé-Zé, L. & Tenreiro, R. ( 2007; ). Congruence of evolutionary relationships inside the LeuconostocOenococcusWeissella clade assessed by phylogenetic analysis of the 16S rRNA gene, dnaA, gyrB, rpoC and dnaK. Int J Syst Evol Microbiol 57, 276–286.[CrossRef]
    [Google Scholar]
  7. Crosa, J. H., Brenner, D. J. & Falkow, S. ( 1973; ). Use of a single-strand specific nuclease for analysis of bacterial and plasmid deoxyribonucleic acid homo- and heteroduplexes. J Bacteriol 115, 904–911.
    [Google Scholar]
  8. Cubero, J. & Graham, J. H. ( 2004; ). The leucine-responsive regulatory protein (lrp) gene for characterization of the relationship among Xanthomonas species. Int J Syst Evol Microbiol 54, 429–437.[CrossRef]
    [Google Scholar]
  9. Da Silva, A. C., Ferro, J. A., Reinach, F. C., Farah, C. S., Furlan, L. R., Quaggio, R. B., Monteiro-Vitorello, C. B., Van Sluys, M. A., Almeida, N. F. & other authors ( 2002; ). Comparison of the genomes of two Xanthomonas pathogens with differing host specificities. Nature 417, 459–463.[CrossRef]
    [Google Scholar]
  10. Doidge, E. M. ( 1915; ). A bacterial disease of the mango. Bacillus mangiferae n. sp. Ann Appl Biol 2, 1–44.[CrossRef]
    [Google Scholar]
  11. Dye, D. W., Bradbury, J. F., Goto, M., Hayward, A. C., Lelliott, R. A. & Schroth, M. N. ( 1980; ). International standards for naming pathovars of phytopathogenic bacteria and a list of pathovar names and pathotype strains. Rev Plant Pathol 59, 153–168.
    [Google Scholar]
  12. 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]
  13. Gagnevin, L. & Pruvost, O. ( 2001; ). Epidemiology and control of mango bacterial black spot. Plant Dis 85, 928–935.[CrossRef]
    [Google Scholar]
  14. Gascuel, O. ( 1997; ). Concerning the NJ algorithm and its unweighted version UNJ. In Mathematical Hierarchies and Biology, pp. 149–171. Edited by B. Mirkin, F. R. McMorris, F. Roberts & A. Rzhetsky. Providence, RI: American Mathematical Society.
  15. Gevers, D., Cohan, F. M., Lawrence, J. G., Spratt, B. G., Coenye, T., Feil, E. J., Stackebrandt, E., Van de Peer, Y., Vandamme, P. & other authors ( 2005; ). Re-evaluating prokaryotic species. Nat Rev Microbiol 3, 733–739.[CrossRef]
    [Google Scholar]
  16. Goncalves, 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]
  17. Grimont, P. A. D. ( 1988; ). Use of DNA reassociation in bacterial classification. Can J Microbiol 34, 541–546.[CrossRef]
    [Google Scholar]
  18. Grimont, P. A. D., Popoff, M. Y., Grimont, F., Coynault, C. & Lemelin, M. ( 1980; ). Reproducibility and correlation study of three deoxyribonucleic acid hybridization procedures. Curr Microbiol 4, 325–330.[CrossRef]
    [Google Scholar]
  19. Guindon, S. & Gascuel, O. ( 2003; ). A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52, 696–704.[CrossRef]
    [Google Scholar]
  20. Hanage, W. P., Fraser, C. & Spratt, B. G. ( 2005a; ). Fuzzy species among recombinogenic bacteria. BMC Biol 3, 6 [CrossRef]
    [Google Scholar]
  21. Hanage, W. P., Kaijalainen, T., Herva, E., Saukkoriipi, A., Syrjänen, R. & Spratt, B. G. ( 2005b; ). Using multilocus sequence data to define the pneumococcus. J Bacteriol 187, 6223–6230.[CrossRef]
    [Google Scholar]
  22. Hauben, L., Vauterin, L., Swings, J. & Moore, E. R. B. ( 1997; ). Comparison of 16S ribosomal DNA sequences of all Xanthomonas species. Int J Syst Bacteriol 47, 328–335.[CrossRef]
    [Google Scholar]
  23. Hong, Y., Garcia, M., Levisohn, S., Lysnyansky, I., Leiting, V., Savelkoul, P. H. M. & Kleven, S. H. ( 2005; ). Evaluation of amplified fragment length polymorphism for differentiation of avian Mycoplasma species. J Clin Microbiol 43, 909–912.[CrossRef]
    [Google Scholar]
  24. Huelsenbeck, J. P. & Ronquist, F. ( 2001; ). mrbayes: Bayesian inference of phylogenetic trees. Bioinformatics 17, 754–755.[CrossRef]
    [Google Scholar]
  25. Huys, G., Rigouts, L., Chemlal, K., Portaels, F. & Swings, J. ( 2000; ). Evaluation of amplified fragment length polymorphism analysis for inter- and intraspecific differentiation of Mycobacterium bovis, M. tuberculosis, and M. ulcerans. J Clin Microbiol 38, 3675–3680.
    [Google Scholar]
  26. Janssen, P., Coopman, R., Huys, G., Swings, J., Bleeker, M., De Vos, P., Zabeau, M. & Kersters, K. ( 1996; ). Evaluation of the DNA fingerprinting method AFLP as a new tool in bacterial taxonomy. Microbiology 142, 1881–1893.[CrossRef]
    [Google Scholar]
  27. Johnson, J. L. ( 1984; ). Nucleic acids in bacterial classification. In Bergey's Manual of Systematic Bacteriology, vol. 1, pp. 8–11. Edited by N. R. Krieg & J. G. Holt. Baltimore: Williams & Wilkins.
  28. 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]
  29. Jones, J. B., Lacy, G. H., Bouzar, H., Stall, R. E. & Schaad, N. W. ( 2006; ). Xanthomonas euvesicatoria sp. nov., Xanthomonas gardneri nom. rev., comb. nov. and Xanthomonas perforans sp. nov. In List of New Names and New Combinations Previously Effectively, but not Validly, Published, Validation List no. 109. Int J Syst Evol Microbiol 56, 925–927.[CrossRef]
    [Google Scholar]
  30. 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]
  31. Kumar, S., Tamura, K. & Nei, M. ( 2004; ). mega3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5, 150–163.[CrossRef]
    [Google Scholar]
  32. Lapage, S. P., Sneath, P. H. A., Lessel, E. F., Skerman, V. B. D., Seelinger, H. P. R. & Clark, W. A. (editors) ( 1992; ). International Code of Nomenclature of Bacteria (1990 Revision) Bacteriological Code. Washington, DC: American Society for Microbiology.
  33. Leal-Klevezas, D. S., Martinez-de-la-Vega, O., Ramirez-Barba, E. J., Osterman, B., Martinez-Soriano, J. P. & Simpson, J. ( 2005; ). Genotyping of Ochrobactrum spp. by AFLP analysis. J Bacteriol 187, 2537–2539.[CrossRef]
    [Google Scholar]
  34. Martens, M., Delaere, M., Coopman, R., De Vos, P., Gillis, M. & Willems, A. ( 2007; ). Multilocus sequence analysis of Ensifer and related taxa. Int J Syst Evol Microbiol 57, 489–503.[CrossRef]
    [Google Scholar]
  35. Martin, D. P., Williamson, C. & Posada, D. ( 2005; ). RDP2: recombination detection and analysis from sequence alignments. Bioinformatics 21, 260–262.[CrossRef]
    [Google Scholar]
  36. Moore, E. R. B., Kruger, A. S., Hauben, L., Seal, S. E., De Baere, R., De Wachter, R., Timmis, K. N. & Swings, J. ( 1997; ). 16S rRNA gene sequence analyses and inter- and intrageneric relationships of Xanthomonas species and Stenotrophomonas maltophilia. FEMS Microbiol Lett 151, 145–153.[CrossRef]
    [Google Scholar]
  37. Mougel, C., Thioulouse, J., Perrière, G. & Nesme, X. ( 2002; ). A mathematical method for determining genome divergence and species delineation using AFLP. Int J Syst Evol Microbiol 52, 573–586.
    [Google Scholar]
  38. Nei, M. & Gojobori, T. ( 1986; ). Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol 3, 418–426.
    [Google Scholar]
  39. Nesme, X., Vaneechoutte, M., Orso, S., Hoste, B. & Swings, J. ( 1995; ). Diversity and genetic relatedness within genera Xanthomonas and Stenotrophomonas using restriction endonuclease site differences of PCR-amplified 16S rRNA gene. Syst Appl Microbiol 18, 127–135.[CrossRef]
    [Google Scholar]
  40. On, S. L. W., Harrington, C. S. & Atabay, H. I. ( 2003; ). Differentiation of Arcobacter species by numerical analysis of AFLP profiles and description of a novel Arcobacter from pig abortions and turkey faeces. J Appl Microbiol 95, 1096–1105.[CrossRef]
    [Google Scholar]
  41. Paradis, E. ( 2006; ). Analysis of Phylogenetics and Evolution with R. New York: Springer.
  42. Patel, M. K., Kulkarni, Y. S. & Moniz, L. ( 1948a; ). Pseudomonas mangiferae-indicae, pathogenic on mango. Indian Phytopathol 1, 147–152.
    [Google Scholar]
  43. Patel, M. K., Moniz, L. & Kulkarni, Y. S. ( 1948b; ). A new bacterial disease of Mangifera indica L. Curr Sci 6, 189–190.
    [Google Scholar]
  44. Portier, P., Fischer-Le Saux, M., Mougel, C., Lerondelle, C., Chapulliot, D., Thioulouse, J. & Nesme, X. ( 2006; ). Identification of genomic species in Agrobacterium biovar 1 by AFLP genomic markers. Appl Environ Microbiol 72, 7123–7131.[CrossRef]
    [Google Scholar]
  45. Rademaker, J. L. W., Hoste, B., Louws, F. J., Kersters, K., Swings, J., Vauterin, L., Vauterin, P. & De Bruijn, F. J. ( 2000; ). Comparison of AFLP and rep-PCR genomic fingerprinting with DNA–DNA homology studies: Xanthomonas as a model system. Int J Syst Evol Microbiol 50, 665–677.[CrossRef]
    [Google Scholar]
  46. 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]
  47. Richter, D., Postic, D., Sertour, N., Livey, I., Matuschka, F. R. & Baranton, G. ( 2006; ). Delineation of Borrelia burgdorferi sensu lato species by multilocus sequence analysis and confirmation of the delineation of Borrelia spielmanii sp. nov. Int J Syst Evol Microbiol 56, 873–881.[CrossRef]
    [Google Scholar]
  48. Robbs, C. F., Ribeiro, R. D. L. D. & Kimura, O. ( 1974; ). Sobre a posicao taxonomica de Pseudomonas mangiferaeindicae Patel et al. 1948, agente causal da “mancha bacteriana” das folhas da mangueira (Mangifera indica L.). Arq Univ Fed Rur Rio de Janeiro 4, 11–14 (in Portuguese).
    [Google Scholar]
  49. Rott, P., Chatenet, M., Granier, M. & Baudin, P. ( 1988; ). L'échaudure des feuilles de canne à sucre provoquée par Xanthomonas albilineans (Ashby) Dowson. II. Diagnostic et spectres d'hôtes de l'agent pathogène en Afrique tropicale. Agron Trop 43, 244–251 (in French).
    [Google Scholar]
  50. Roumagnac, P., Gagnevin, L., Gardan, L., Sutra, L., Manceau, C., Dickstein, E. R., Jones, J. B., Rott, P. & Pruvost, O. ( 2004; ). Polyphasic characterization of xanthomonads isolated from onion, garlic and Welsh onion (Allium spp.) and their relatedness to different Xanthomonas species. Int J Syst Evol Microbiol 54, 15–24.[CrossRef]
    [Google Scholar]
  51. Rozas, J., Sanchez-Del Barrio, J. C., Messeguer, X. & Rozas, R. ( 2003; ). DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19, 2496–2497.[CrossRef]
    [Google Scholar]
  52. Saitou, N. & Nei, M. ( 1987; ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–425.
    [Google Scholar]
  53. 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]
  54. Schaad, N. W., Postnikova, E., Lacy, G. H., Sechler, A., Agarkova, I., Stromberg, P. E., Stromberg, V. K. & Vidaver, A. K. ( 2006; ). Emended classification of xanthomonad pathogens on citrus. Syst Appl Microbiol 29, 690–695.[CrossRef]
    [Google Scholar]
  55. Schaad, N. W., Postnikova, E., Lacy, G. H., Sechler, A., Agarkova, I., Stromberg, P. E., Stromberg, V. K. & Vidaver, A. K. ( 2007; ). Xanthomonas alfalfae sp. nov., nom. rev. and others. 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]
  56. Shimodaira, M. & Hasegawa, M. ( 1999; ). Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol Biol Evol 16, 1114–1116.[CrossRef]
    [Google Scholar]
  57. Stackebrandt, E., Frederiksen, W., Garrity, G. M., Grimont, P. A. D., Kämpfer, P., Maiden, M. C. J., Nesme, X., Rosselló-Mora, R., Swings, J. & other authors ( 2002; ). Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol Microbiol 52, 1043–1047.[CrossRef]
    [Google Scholar]
  58. Swings, J. G. & Civerolo, E. L. (editors) ( 1993; ). Xanthomonas. London: Chapman & Hall.
  59. Tajima, F. ( 1989; ). Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123, 585–595.
    [Google Scholar]
  60. Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F. & Higgins, D. G. ( 1997; ). The clustal_x windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25, 4876–4882.[CrossRef]
    [Google Scholar]
  61. Thompson, F. L., Li, Y., Gomez-Gil, B., Thompson, C. C., Hoste, B., Vandemeulebroecke, K., Rupp, G. S., Pereira, A., De Bem, M. M. & other authors ( 2003; ). Vibrio neptunius sp. nov., Vibrio brasiliensis sp. nov. and Vibrio xuii sp. nov., isolated from the marine aquaculture environment (bivalves, fish, rotifers and shrimps). Int J Syst Evol Microbiol 53, 245–252.[CrossRef]
    [Google Scholar]
  62. Trébaol, G., Gardan, L., Manceau, C., Tanguy, J. L., Tirilly, Y. & Boury, S. ( 2000; ). Genomic and phenotypic characterization 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]
  63. Vauterin, L., Hoste, B., Kersters, K. & Swings, J. ( 1995; ). Reclassification of Xanthomonas. Int J Syst Bacteriol 45, 472–489.[CrossRef]
    [Google Scholar]
  64. Wayne, L. G., Brenner, D. J., Colwell, R. R., Grimont, P. A. D., Kandler, O., Krichevsky, M. I., Moore, L. H., Moore, W. E. C., Murray, R. G. E. & 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]
  65. Young, J. M., Takikawa, Y., Gardan, L. & Stead, D. E. ( 1992; ). Changing concepts in the taxonomy of plant pathogenic bacteria. Annu Rev Phytopathol 30, 67–105.[CrossRef]
    [Google Scholar]
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