The X. campestris pv. raphani (Xcr) 756C and X. oryzae pv. oryzicola (Xoc) BLS256 genomes. Rings illustrate, from outside to inside, genome coordinates (kb), protein-coding genes in forward (outer) and reverse strands, IS elements (black), TAL effector genes (yellow), tRNA (blue) and rRNA (red) genes, percent G+C content, and GC skew. GC skew shows (G − C)/(G + C) in 10-kb windows; positive values indicate the leading strand of replication, and negative values indicate the lagging strand. Protein-coding genes specific and essential (see text) to the strains in Table 1 that are pathogenic to dicots are highlighted (green) in the X. campestris pv. raphani circle, and those specific to pathogens of monocots are highlighted in the X. oryzae pv. oryzicola circle.

Phylogenomic relationships among sequenced Xanthomonas strains. A maximum likelihood tree based on a set of 31 conserved phylogenomic marker genes (see text) is shown. Bootstrap values are displayed at nodes. Stenotrophomonas maltophilia strain K279a (SmaK) was used as an outgroup. XooK, XooM, XooP, X. oryzae pv. oryzae strains KACC10331, MAFF311018, and PXO99^A, respectively; Xoc, X. oryzae pv. oryzicola BLS256; Xcv, Xanthomonas axonopodis pv. vesicatoria 85-10; Xac, X. axonopodis pv. citri 306; Xac, X. campestris pv. raphani 756C; XccB, Xcc8, and XccA, X. campestris pv. campestris strains 8004, ATCC33913, and B100, respectively.

Alignments of the X. campestris pv. raphani 756C and X. oryzae pv. oryzicola BLS256 genomes to those of their vascular counterparts. (A) Whole-genome alignments of X. campestris pv. raphani 756C with X. campestris pv. campestris 8004, X. campestris pv. campestris ATCC 33913, and X. campestris pv. campestris B100; (B) whole-genome alignments of X. oryzae pv. oryzicola BLS256 with X. oryzae pv. oryzae KACC10331, X. oryzae pv. oryzae MAFF311018, and X. oryzae pv. oryzae PXO99^A. Alignments were generated using the MAUVE program (18) with default parameters. Locally colinear blocks, shown as rounded rectangles, represent regions without rearrangement of homologous sequence across genomes. The orientation of the locally colinear blocks, forward or reverse, is indicated by their position above or below the line, respectively. Lines between genomes trace orthologous locally colinear blocks. The minimum locally colinear block weight and the number of locally colinear blocks are shown for each alignment. Inside each locally colinear block, vertical bars represent the average level of conservation of sequence across genomes.

Phylogenetic analysis of TAL effector genes in three X. oryzae strains. Displayed is the phylogeny for the DNA alignment of 60 TAL effector genes from X. oryzae pv. oryzicola BLS256, X. oryzae pv. oryzae MAFF 311018, and X. oryzae pv. oryzae PXO99^A. Gene names are preceded by B, M, or P, respectively, to denote their origin and are designated according to Salzberg et al. (74). X. oryzae pv. oryzae KACC10331 TAL effector genes were not included (see text). An unrooted tree was estimated by the Phyml program using 100 bootstrap replicates and the TPM1uf +I+G model. The tree is shown rooted at the outgroup, which is the pthA gene sequence from X. axonopodis pv. citri 306.

Distribution of homologous protein clusters specific and essential to different categories of sequenced Xanthomonas strains. The cluster sets are not refined; i.e., the numbers are based on annotated genes and include clusters formed by distinct sets of paralogs.