Figure 5.

Circular genome maps of P. fluorescens strains SBW25 and Pf0-1. (a) P. fluorescens SBW25. From the outside in, the outer most circle shows atypical regions (blue boxes) and prophage-like regions (pink boxes) numbered according to Supplementary Table 3 in Additional data file 3; circle 2, scale line (in Mbps); circles 3 and 4 show the position of CDSs transcribed in a clockwise and anticlockwise direction, respectively (for color codes, see below); circle 5, location of IVET EIL fusions (black); circle 6, graph showing density of CDSs with orthologues (red) and those unique to SBW25 (green) compared to P. fluorescens Pf0-1 (window size 50,000 bp, step size 200); circle 7, P. fluorescens SBW25 variable region (green line); circle 8, IR1_g inverted repeats (dark blue); circle 9, R0 family of intergenic repeats (navy blue); circle 10, R2 family of intergenic repeats (light blue); circle 11, R5, R30, R178 and R200 families of intergenic repeats (aqua); circle 12, repeat deserts (ReDs; grey boxes); circle 13, GC skew (window 10,000 bp). CDSs were color-coded according to the function of their gene products: dark green, membrane or surface structures; yellow, central or intermediary metabolism; cyan, degradation of macromolecules; red, information transfer/cell division; cerise, degradation of small molecules; pale blue, regulators; salmon pink, pathogenicity or adaptation; black, energy metabolism; orange, conserved hypothetical; pale green, unknown; and brown, pseudogenes. Note that IR1_g repeats were not included in the ReD analysis because, based on their structure, we could not exclude the possibility that many of them simply represent transcription termination sequences. Where some ReDs appear to contain R-family repeats (for example, ReDs at about 6.1 Mb) there is actually more than one ReD, separated by a very small DNA region, that cannot be resolved in the figure. (b) P. fluorescens Pf0-1. From the outside in, outer most circle shows atypical regions (blue boxes) and prophage-like regions (pink boxes) numbered according to Supplementary Table 4 in Additional data file 3; circle 2, scale line (in Mbps); circles 3 and 4 show the position of CDSs transcribed in a clockwise and anticlockwise direction, respectively (for color codes, see above); circle 5, orthologues of SBW25 EIL - those EIL that are antisense in SBW25 are indicated by orthologues to the predicted CDSs on the sense strand; circle 6, graph showing density of CDSs with orthologues (red) and those unique to Pf0-1 (green) compared to P. fluorescens SBW25 (window size 50,000 bp, step size 200); circle 7, P. fluorescens Pf0-1 variable region (green line); circle 8, IR1_g inverted repeats (dark blue); circle 9, R5 family of intergenic repeats (navy blue); circle 10, R6 family of intergenic repeats (light blue); circle 11, R0, R1, R6-partial, R26, R30, R69, and R178 families of intergenic repeats (aqua); circle 12, GC skew (window 10,000 bp).

Silby et al. Genome Biology 2009 10:R51   doi:10.1186/gb-2009-10-5-r51
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