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

¹ Central Science Laboratory, Sand Hutton, York YO41 1LZ, UK
² National Agricultural Biotechnology Centre, Kawanda Agricultural Research Institute, PO Box 7065, Kampala, Uganda

Correspondence
Neil Parkinson
n.parkinson{at}csl.gov.uk

The genus Xanthomonas 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 (gyrB) 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 X. albilineans and X. sacchari as the most ancestral species. Three species, X. hyacinthi, X. translucens and X. theicola, formed an early-branching group. Three clades were supported by high bootstrap values: group 1 comprised X. cucurbitae, X. cassavae and X. codiaei; group 2 comprised X. arboricola, X. campestris, X. populi, X. hortorum, X. gardneri and X. cynarae; group 3 contained the remaining species, within which two further clades, supported by a 100 % bootstrap value, were identified. Group 3A comprised X. axonopodis, X. euvesicatoria, X. perforans and X. melonis, together with X. alfalfae, X. citri and X. fuscans, whose names were recently validly published. Group 3B contained the monocot pathogens X. vasicola and X. oryzae. Two recently identified species, X. cynarae and X. gardneri, were poorly discriminated and were related closely to X. hortorum. Three species, X. perforans, X. euvesicatoria and X. alfalfae, had identical gyrB 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 (n=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.

Supplementary tables showing type strains of all xanthomonad species used in the study, PCR and sequencing primers and a similarity matrix indicating all inter-species percentage nucleotide identities are available with the online version of this paper.

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				N. Parkinson, C. Cowie, J. Heeney, and D. Stead Phylogenetic structure of Xanthomonas determined by comparison of gyrB sequences Int J Syst Evol Microbiol, February 1, 2009; 59(2): 264 - 274. [Abstract] [Full Text] [PDF]