Color Plates
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Editors:
Mark J. Pallen1,
Karen E. Nelson2,
Gail M. Preston3
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Affiliations:
1: University of Birmingham Birmingham, United Kingdom;
2: Department of Biology Howard University Washington, DC and The Institute for Genomic Research Rockville, Maryland;
3: Oxford University Oxford, United Kingdom
Content Type: Monograph
Source:
Bacterial Pathogenomics
Publication Year:
2007
Category: Genomics and Bioinformatics; Bacterial Pathogenesis
e-ISBN
:
9781555815530
Book DOI:
10.1128/9781555815530
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Figures
Color Plates
Citation:
Pallen M, Nelson K, Preston G.
2007.
Color Plates,
In
Bacterial Pathogenomics.
ASM Press, Washington, DC.
/content/10.1128/9781555815530.bm1.bm01fig01
COLOR PLATE 1
Circular representation of closed C. jejuni 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 C. jejuni-specific and C. jejuni RM1221-specific ORFs. The sixth circle plots atypical regions (χ2 value). The seventh circle denotes tRNA, rRNA, and sRNA (tmRNA and 4.5S RNA) loci.
10.1128/9781555815530/ps1-01_thmb.gif
10.1128/9781555815530/ps1-01.gif
Click to view
COLOR PLATE 1
Circular representation of closed C. jejuni 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 C. jejuni-specific and C. jejuni RM1221-specific ORFs. The sixth circle plots atypical regions (χ2 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.
/content/10.1128/9781555815530.bm1.bm01fig02
COLOR PLATE 2
Whole-genome comparison of five Campylobacter 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 (C. jejuni RM1221, x axis) and query (C. jejuni NCTC 11168 [upper y axis] and C. coli RM2228 [lower y 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 Campylobacter strains (B) and for members of the sequenced ε-Proteobacteria (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 C. jejuni 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 C. jejuni RM1221 reference sequences were plotted.
10.1128/9781555815530/ps2-01_thmb.gif
10.1128/9781555815530/ps2-01.gif
Click to view
COLOR PLATE 2
Whole-genome comparison of five Campylobacter 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 (C. jejuni RM1221, x axis) and query (C. jejuni NCTC 11168 [upper y axis] and C. coli RM2228 [lower y 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 Campylobacter strains (B) and for members of the sequenced ε-Proteobacteria (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 C. jejuni 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 C. jejuni RM1221 reference sequences were plotted.
Citation:
Pallen M, Nelson K, Preston G.
2007.
Color Plates,
In
Bacterial Pathogenomics.
ASM Press, Washington, DC.
/content/10.1128/9781555815530.bm1.bm01fig03
COLOR PLATE 3
Pathogenicity by the permutation principle. (Left) Genome maps of different S. pyogenes 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.
10.1128/9781555815530/ps4-01_thmb.gif
10.1128/9781555815530/ps4-01.gif
Click to view
COLOR PLATE 3
Pathogenicity by the permutation principle. (Left) Genome maps of different S. pyogenes 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.
/content/10.1128/9781555815530.bm1.bm01fig04
COLOR PLATE 4
Circular genome maps of L. monocytogenes EGDe and L. innocua CLIP11262 showing the position and orientation of genes. From the outside: circles 1 and 2, L. innocua and L. monocytogenes genes on the + and – strands, respectively; circle 3, G/C bias (G+C/G–C) of L. monocytogenes; circle 4, G+C content of L. monocytogenes 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., Science
294:849–852, 2001).
10.1128/9781555815530/ps5-01_thmb.gif
10.1128/9781555815530/ps5-01.gif
Click to view
COLOR PLATE 4
Circular genome maps of L. monocytogenes EGDe and L. innocua CLIP11262 showing the position and orientation of genes. From the outside: circles 1 and 2, L. innocua and L. monocytogenes genes on the + and – strands, respectively; circle 3, G/C bias (G+C/G–C) of L. monocytogenes; circle 4, G+C content of L. monocytogenes 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., Science 294:849–852, 2001).
Citation:
Pallen M, Nelson K, Preston G.
2007.
Color Plates,
In
Bacterial Pathogenomics.
ASM Press, Washington, DC.
/content/10.1128/9781555815530.bm1.bm01fig05
COLOR PLATE 5
Circular diagram of Erwinia carotovora subsp. atroseptica (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: Yersinia pestis CO92, Escherichia coli CFT073, Salmonella enterica serovar Typhi CT18, Pseudomonas putida KT2440, Pseudomonas syringae pv. tomato DC3000, Xanthomonas campestris pv. campestris ATCC 33913, Xylella fastidiosa Temecula1, Ralstonia solanacearum GMI1000, Xylella fastidiosa 9a5c, Xanthomonas oryzae pv. oryzae KACC10331, Xanthomonas axonopodis pv. citri 306, Bradyrhizobium japonicum USDA 110, Mesorhizobium loti MAFF303099, Agrobacterium tumefaciens C58, Sinorhizobium meliloti 1021, onion yellows phytoplasma OY-M, Leifsonia xyli subsp. xyli 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 Pseudomonas syringae pv. tomato DC3000. (B) Type III secretion system. (C) Nitrogen fixation and the Rhizobiaceae.
10.1128/9781555815530/ps6-01_thmb.gif
10.1128/9781555815530/ps6-01.gif
Click to view
COLOR PLATE 5
Circular diagram of Erwinia carotovora subsp. atroseptica (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: Yersinia pestis CO92, Escherichia coli CFT073, Salmonella enterica serovar Typhi CT18, Pseudomonas putida KT2440, Pseudomonas syringae pv. tomato DC3000, Xanthomonas campestris pv. campestris ATCC 33913, Xylella fastidiosa Temecula1, Ralstonia solanacearum GMI1000, Xylella fastidiosa 9a5c, Xanthomonas oryzae pv. oryzae KACC10331, Xanthomonas axonopodis pv. citri 306, Bradyrhizobium japonicum USDA 110, Mesorhizobium loti MAFF303099, Agrobacterium tumefaciens C58, Sinorhizobium meliloti 1021, onion yellows phytoplasma OY-M, Leifsonia xyli subsp. xyli 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 Pseudomonas syringae pv. tomato DC3000. (B) Type III secretion system. (C) Nitrogen fixation and the Rhizobiaceae.
Citation:
Pallen M, Nelson K, Preston G.
2007.
Color Plates,
In
Bacterial Pathogenomics.
ASM Press, Washington, DC.
/content/book/10.1128/9781555815530.bm1
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