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Fig. 8.1 GAS Genome alignments. The seven available GAS genomes were compared using the software package Mauve, a method that identifies conserved genomic regions, rearrangements and inversions in conserved regions, and the exact sequence breakpoints of such rearrangements across multiple genomes [11]. Corresponding regions share the same color and are connected by lines. Colli-near regions are positioned above the central axis (relative to M1) while inverted regions are drawn below the axis. Light gray regions were too divergent in at least one genome to be meaningfully aligned. (This figure also appears on page 153.)

Mauve Genome Alignment

Fig. 8.2 GAS vs S. uberis alignment. The corresponding regions in the M1 and S. uberis genomes identified by Mauve analysis are shown. Several large regions of collinearity are evident between the two species. Corresponding regions share the same color and are connected by lines. (This figure also appears on page 157.)

Fig. 8.2 GAS vs S. uberis alignment. The corresponding regions in the M1 and S. uberis genomes identified by Mauve analysis are shown. Several large regions of collinearity are evident between the two species. Corresponding regions share the same color and are connected by lines. (This figure also appears on page 157.)

Sccmec Iii And

Fig. 9.1 Structure of type I, II, III, and IV staphylococcal cassette chromosome mec (SCCmec) elements (adapted from [70]). SCCmec is characterized by two common gene complexes, the ccr (cassette chromosome recombinase) gene complex (gray) and the mec gene complex (blue). Integrated IS43 7, Tn554, and plasmid pT181 are also indicated. Gene symbols: cad, cadmium

Fig. 9.1 Structure of type I, II, III, and IV staphylococcal cassette chromosome mec (SCCmec) elements (adapted from [70]). SCCmec is characterized by two common gene complexes, the ccr (cassette chromosome recombinase) gene complex (gray) and the mec gene complex (blue). Integrated IS43 7, Tn554, and plasmid pT181 are also indicated. Gene symbols: cad, cadmium resistance; ccr, cassette chromosome recombinase; ermA, erythromycin resistance; hsdR, host specificity determinant; kdp, two-component system regulating potassium transport; mec, penicillin binding protein 2a, methicillin resistance; mer, mercury resistance; tetK, tetracycline resistance. (This figure also appears on page 191.)

Synteny Analysis Artemis

Fig. 9.2 Pairwise comparison of the Staphylococcus epidermidis ATCC 12228 and Staphylococcus epidermidis RP62A genomes displayed using the Artemis Comparison Tool (ACT; http:// www.sanger.ac.uk/Software/ACT). The red bars represent homologous matches between the genomes and the blue bars indicate a homologous, but inverted chromosomal region.

Fig. 9.2 Pairwise comparison of the Staphylococcus epidermidis ATCC 12228 and Staphylococcus epidermidis RP62A genomes displayed using the Artemis Comparison Tool (ACT; http:// www.sanger.ac.uk/Software/ACT). The red bars represent homologous matches between the genomes and the blue bars indicate a homologous, but inverted chromosomal region.

Genomic islands, IS elements, phages, SCC cassettes, and genes involved in adherence and biofilm formation are marked as colored boxes. Gene symbols: aae, autolysin/adhesin; aap, accumulation-associated protein; atlE, autolysin; bhp, Bap homologous protein; ica, intercellular adhesin. (This figure also appears on page 196.)

Sure Select Sequence Capture
Fig. 11.1 Multiple alignment of the four neisseria! genomes so far fully sequenced using the program Mauve [100]. Locally collinear blocks of DNA are depicted in the same colors and connected via correspondingly colored lines. Equally colored blocks on different sides of black lines corresponding to

the respective genome sequence indicate chromosomal inversions. The chromosomal locations of potential prophages [30], putative genetic islands [13], and some putative virulence genes are given for strain MC58. (This figure also appears on page 235.)

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