Fig. S1 Plot of the Bayesian assignment of Xanthomonas oryzae pv. oryzae (Xoo) and Xanthomonas oryzae pv. oryzicola (Xoc) strains to clusters based on the analysis of the concatenated dataset (glnA, gyrB and rpoD sequences) using the no admixture model of structure 2.1 software. Each haplotype is represented by a line and the geographical origin of the strains is given.

Fig. S2 The type III effector (T3E) XopO is not essential for the virulence and tissue specificity of Xanthomonas oryzae in rice Nipponbare. The bacterial cells were suspended in sterilized water and the cell concentration was adjusted to an optical density at 600 nm (OD600) of 0.2 '2 × 108 colony-forming units (cfu)/mL'. Data shown are the means ± standard deviation from three replications, each with 30 leaves, from one representative experiment; similar results were obtained in the other two independent experiments. (a) Average length of lesions caused by Xanthomonas oryzae pv. oryzicola 7 days post-inoculation. Approximately 20 µL of bacterial culture suspension were infiltrated into leaf mesophyll tissue with a 1-mL blunt-end plastic syringe. (b) Average length of lesions caused by Xanthomonas oryzae pv. oryzae inoculated by the leaf-clipping method, 14 days after inoculation. (c) Average length of lesions caused by Xanthomonas oryzae pv. oryzae inoculated by the leaf infiltration method, 7 days after inoculation.

Table S1 The type III effector (T3E) genes analysed in this study: gene functions and primer sequences used for polymerase chain reaction (PCR) amplifications and for the preparation of probes for dot-blot hybridizations.

Table S2 Polymerase chain reaction (PCR) primers used for the functional analysis of the type III effector (T3E) gene xopO in Xanthomonas oryzae.

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