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Color Plates

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Figures

Image of COLOR PLATE 1

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COLOR PLATE 1

Circular representation of closed RM1221 genome. Each concentric circle represents genomic data and is numbered from the outermost to the innermost circle. Refer to the key for details on color representations. The first and second circles represent predicted ORFs on the positive (+) and negative (–) strands, respectively. The third circle shows the GC skew. The fourth circle depicts genetic loci of interest: CRISPR (clustered regularly interspaced short palindromic repeats), DNA competence, EP, LOS, prophage and genomic island regions, motility, repeats, and type I restriction/modification regions. The fifth circle demarcates -specific and RM1221-specific ORFs. The sixth circle plots atypical regions (χ value). The seventh circle denotes tRNA, rRNA, and sRNA (tmRNA and 4.5S RNA) loci.

Citation: Pallen M, Nelson K, Preston G. 2007. Color Plates, In Bacterial Pathogenomics. ASM Press, Washington, DC.
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Image of COLOR PLATE 2

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COLOR PLATE 2

Whole-genome comparison of five strains. Line figures were the result of PROmer analysis. (A) Colored lines denote percent identity of protein translations and were plotted according to the location in the reference ( RM1221, axis) and query ( NCTC 11168 [upper axis] and RM2228 [lower axis]) genomes. (B and C) The Venn diagrams show the number of proteins shared (black) or unique (red) within a particular relationship for all five strains (B) and for members of the sequenced ε- (C) compared in this study. Protein sequences binned as “unique” are unique within the context of the genomes plotted and the cut-offs used to parse the BLASTP data. The pie charts plot the number of protein sequences by main functional role categories for RM1221 ORFs. (D) A frequency distribution of protein percent identity was computed: specifically, the number of protein sequences within class intervals of 5% amino acid identity from 35 to 100% that match RM1221 reference sequences were plotted.

Citation: Pallen M, Nelson K, Preston G. 2007. Color Plates, In Bacterial Pathogenomics. ASM Press, Washington, DC.
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COLOR PLATE 3

Pathogenicity by the permutation principle. (Left) Genome maps of different strains. Red rectangles are prophages (to scale). (Right) Downstream of the lysis genes (violet), virulence genes (red) are found in the vast majority of the prophages.

Citation: Pallen M, Nelson K, Preston G. 2007. Color Plates, In Bacterial Pathogenomics. ASM Press, Washington, DC.
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COLOR PLATE 4

Circular genome maps of EGDe and CLIP11262 showing the position and orientation of genes. From the outside: circles 1 and 2, and genes on the + and – strands, respectively; circle 3, G/C bias (G+C/G–C) of ; circle 4, G+C content of with higher G+C content indicated by longer bars. The scale in megabases is indicated on the outside of the genomes with the origin of replication being at position 0 (adapted from Glaser et al., 849–852, 2001).

Citation: Pallen M, Nelson K, Preston G. 2007. Color Plates, In Bacterial Pathogenomics. ASM Press, Washington, DC.
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COLOR PLATE 5

Circular diagram of subsp. (strain SCRI1043) genome generated by GenomeDiagram software, showing from outer rings to inner rings: locations of 17 horizontally acquired islands; Eca1043 coding sequences in forward and reverse directions and colored by functional class; reciprocal best hits to coding sequence from plant- and animal-associated bacterial genomes, ordered by overall percentage identity between amino acid sequences: CO92, CFT073, serovar Typhi CT18, KT2440, pv. DC3000, pv. ATCC 33913, Temecula1, GMI1000, 9a5c, pv. KACC10331, pv. 306, USDA 110, MAFF303099, C58, 1021, onion yellows phytoplasma OY-M, subsp. CTCB07. Inner rings indicating reciprocal best hits to coding sequences from other genomes are colored individually on a scale from 30% amino acid identity (cyan) to 70% identity (brick red). Examples of horizontally acquired islands show an increase in the number of coding sequences with reciprocal best hits and/or a high amino acid sequence similarity to plant-associated bacteria (PAB) compared to animal-pathogenic enterobacteria (APE). (A) Coronafacic acid phytotoxin production and pv. DC3000. (B) Type III secretion system. (C) Nitrogen fixation and the .

Citation: Pallen M, Nelson K, Preston G. 2007. Color Plates, In Bacterial Pathogenomics. ASM Press, Washington, DC.
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