Phylogenies based on four loci confirmed the relatedness of all nine validly published species type strains within the Pseudomonas syringae species complex. To further establish the phylogenetic structure within the complex, all 67 pathovar type strains (with defined host ranges) were sequenced using a 578-nucleotide rpoD locus. Since this locus encompassed that used in a previous seven-locus study, it was possible to relate these strains to the existing phylogroup, genomospecies and binomial classifications. All species type strains were distinguished by relatively long branch lengths with all four loci, except for P. savastanoi, P. ficuserectae, P. meliae, P. amygdali and P. tremae, which were attributed to phylogroup 3. The grouping of P. tremae with these genomospecies-2 species was surprising since this species was previously designated as the sole representative of genomospecies 5. The oat pathogen P. syringae pv. coronafaciens was also distinguished by relatively long branch lengths with all four loci. The rpoD phylogeny grouped all the pathovar type strains into major clades that corresponded to previously defined phylogroups, except for two genomospecies-7 strains and P. caricapapayae, which were identified as a new phylogroup (6). There was good correlation between phylogroup and genomospecies classifications, except that two genomospecies-8 strains (P. avellanae and P. syringae pv. theae) were found as a distinct clade within phylogroup 1 along with P. syringae pvs morsprunorum and actinidiae. The rpoD locus will provide a common reference framework to improve monitoring and surveillance of these important pathogens.

Using sequences from the recA locus, we have produced a phylogeny of 188 Dickeya strains from culture collections and identified species relatedness and subspecies clade structure within the genus. Of the six recognized species, Dickeya paradisiaca, D. chrysanthemi and D. zeae were discriminated with long branch lengths. The clade containing the D. paradisiaca type strain included just one additional strain, isolated from banana in Colombia. Strains isolated from Chrysanthemum and Parthenium species made up most of the clade containing the D. chrysanthemi type strain, and the host range of this species was extended to include potato. The D. zeae clade had the largest number of sequevars and branched into two major sister clades that contained all of the Zea mays isolates, and were identified as phylotypes PI and PII. The host range was increased from six to 13 species, including potato. The recA sequence of an Australian sugar-cane strain was sufficiently distinct to rank as a new species-level branch. In contrast to these species, Dickeya dadantii, D. dianthicola and D. dieffenbachiae were distinguished with shorter branch lengths, indicating relatively closer relatedness. The recA sequence for the type strain of D. dadantii clustered separately from other strains of the species. However, sequence comparison of three additional loci revealed that the D. dadantii type strain grouped together with the six other D. dadantii strains that were sequenced. Analysis of all four loci indicated that the D. dadantii strains were most closely related to D. dieffenbachiae. Three further branches (DUC-1, -2 and -3) were associated with these three species, which all diverged from a common origin and can be considered as a species complex. The large clade containing the D. dianthicola type strain comprised 58 strains and had little sequence diversity. One sequevar accounted for the majority of these strains, which were isolated nearly exclusively from eight hosts from Europe. Isolation of this sequevar on multiple occasions from Dianthus and (more recently) potato demonstrates that this lineage has become established in these species. The D. dadantii clade comprised 11 sequevars, and the known host range of the species was extended from eight to 19 species. New hosts included several ornamental species and potato. The clade DUC-1 was made up exclusively of potato strains originating from Europe, which had identical sequences, whilst DUC-2 strains were isolated mostly from a variety of monocotyledonous species. A single strain from Aglaonema sp. made up DUC-3. A single sequevar constituted the D. dieffenbachiae clade. The phylogenetic method described will provide a simple means for identification to the species and intraspecies level, which will support efforts to control these pathogens based on monitoring and surveillance.

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 (n521) 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. INTRODUCTIONClassification of species within the genus Xanthomonas, which was hitherto based on biochemical characteristics (Van den Mooter & Swings, 1990), underwent major revision after a comprehensive spectrophotometric DNA-DNA hybridization study of the genus (Vauterin et al., 1995), which resulted in the recognition of 20 constituent species. Following this study, names of seven further species have been validly published: X. cynarae (Trébaol et al., 2000), X. euvesicatoria, X. perforans, X. gardneri (Jones et al., 2004; Euzéby, 2006), X. citri, X. fuscans and X. alfalfae (Gabriel et al., 1989; Euzéby, 2007;Schaad et al., 2005Schaad et al., , 2006Schaad et al., , 2007.The complexity of the genus and resource requirements for comprehensive pairwise analyses required for DNA-DNA hybridization analysis make this technique unsuitable for routine identification in most diagnostic laboratories. A rapid characterization method based on analysing cell-wall fatty acids using GC was developed and applied to the identification of plant pathogens (Stead, 1989(Stead, , 1992. Whilst this method can be very useful for typing of some xanthomonads, it does not provide the necessary resolution or reproducibility to be useful for all species. More recently, a majo...

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b Variable-number tandem-repeat (VNTR) analysis was used for high-resolution discrimination among Ralstonia solanacearum phylotype IIB sequevar 1 (PIIB-1) isolates and further evaluated for use in source tracing. Five tandem-repeat-containing loci (comprising six tandem repeats) discriminated 17 different VNTR profiles among 75 isolates from potato, geranium, bittersweet (Solanum dulcamara), tomato, and the environment. R. solanacearum isolates from crops at three unrelated outbreak sites where river water had been used for irrigation had distinct VNTR profiles that were shared with PIIB-1 isolates from infected bittersweet growing upriver of each site. The VNTR profiling results supported the implication that the source of R. solanacearum at each outbreak was contaminated river water. Analysis of 51 isolates from bittersweet growing in river water at different locations provided a means to evaluate the technique for studying the epidemiology of the pathogen in the environment. Ten different VNTR profiles were identified among bittersweet PIIB-1 isolates from the River Thames. Repeated findings of contiguous river stretches that produced isolates that shared single VNTR profiles supported the hypothesis that the pathogen had disseminated from infected bittersweet plants located upriver. VNTR profiles shared between bittersweet isolates from two widely separated Thames tributaries (River Ray and River Colne) suggested they were independently contaminated with the same clonal type. Some bittersweet isolates had VNTR profiles that were shared with potato isolates collected outside the United Kingdom. It was concluded that VNTR profiling could contribute to further understanding of R. solanacearum epidemiology and assist in control of future disease outbreaks.