Circular representations of the X. campestris pv. vesicatoria strain 85-10 chromosome displaying relevant genome features (A and B) and validation of the sequence assembly by a fosmid map (B). (A) From the outer to the inner concentric circle: circle 1, genomic position in kilobases; circles 2 and 3, predicted CDS on the forward (outer wheel) and the reverse (inner wheel) strands colored according to the assigned COG classes; circles 4, 5, and 6, CDS with homologs in the chromosomes of X. axonopodis pv. citri (pink), X. campestris pv. campestris (dark blue), and X. oryzae pv. oryzae (light blue), respectively; circle 7, the G+C content showing deviations from the average (64.75%); circle 8, GC skew. The bar below the circles represents the COG colors for the functional groups (C, energy production and conversion; D, cell cycle control, mitosis, and meiosis; E, amino acid transport and metabolism; F, nucleotide transport and metabolism; G, carbohydrate transport and metabolism; H, coenzyme transport and metabolism; I, lipid transport and metabolism; J, translation; K, transcription; L, replication, recombination, and repair; M, cell wall/membrane biogenesis; N, cell motility; O, posttranslational modification, protein turnover, and chaperones; P, inorganic ion transport and metabolism; Q, secondary metabolite biosynthesis, transport, and catabolism; R, general function prediction only; S, function unknown; T, signal transduction mechanisms; U, intracellular trafficking and secretion; V, defense mechanisms). (B) Fosmid map of the X. campestris pv. vesicatoria chromosome. Each green arc represents a single fosmid clone mapped onto the assembled sequence; circle 1, coverage of the X. campestris pv. vesicatoria chromosome with fosmid clones (green indicates that the chromosome is covered by more than one fosmid clone, and yellow indicates that the chromosome is covered by one fosmid clone.); circle 2, genes coding for the different secretion systems and the flagellar gene cluster (red, Sec and TAT pathway; black, putative type I secretion system; blue, type II secretion systems; magenta, type III secretion system; green, type IV system components; brown, flagellar system); circle 3, complete IS elements; circle 4, tRNA genes (green) and the two rRNA operons (blue).

Comparison between three effector integron regions of the X. campestris pv. vesicatoria genome. Schematic overview of the chromosomal (A) xopC, (B) XCV2280, and (C) the avrBs1 region on plasmid pXCV183. Gray shaded regions indicate DNA identities of at least 80%, and red marks indicate CDS with low G+C content. Single-headed arrows represent CDS and the direction of transcription. Red arrows refer to putative effector genes. Green CDS are related to mobile genetic elements. Green double-headed arrows represent IS elements, black arrows represent a putative postsegregational killing system, and white arrows represent genes of unknown function. Blue triangles refer to 62-bp inverted repeats. Black rectangles correspond to direct repeats. A jagged line in a CDS indicates frame shifts. The G+C content of the xopC and avrBs1 region was calculated for 100-bp windows (65% on average) and is displayed at the bottom.

Comparison of the chromosomal sequences of (A) X. axonopodis pv. citri (Xac), X. campestris pv. vesicatoria (Xcv), and X. campestris pv. campestris (Xcc) and (B) X. campestris pv. vesicatoria (Xcv) and X. oryzae pv. oryzae (Xoo) using ACT. Red lines indicate DNA sequences longer than 400 bp with at least 80% identity. The darker the color, the higher the DNA identity. Numbers mark the locations of different gene clusters on the chromosomes, which encode (1) the hrp type III secretion system, (2) the xcs type II secretion system, (3) the flagellar system, and (4) the xps type II secretion system. Dashed lines highlight the less-conserved region in the middle of the X. campestris pv. vesicatoria, X. axonopodis pv. citri, and X. campestris pv. campestris chromosomes.