Circular representation of the S. flexneri 2a 2457T genome and comparison with the E. coli K-12 genome. The outer circle shows the distribution of all ORFs. Blue represents ORFs in backbone regions with sequence identity to K-12, brown represents ORFs in S. flexneri-specific islands, and pink represents IS ORFs. The location outside or inside the axis denotes the direction of transcription. The second circle shows the IS elements; the predominant IS, IS1, is blue. Arrows in the third and fourth circles indicate rRNA (red) and tRNA (green). The fifth circle gives the genome scale in base pairs. The sixth circle shows the C/G skew calculated for each sliding window of 10 kb. In the comparison between S. flexneri 2a 2457T (seventh circle) and E. coli K-12 (the innermost circle), the segments in 2457T that are above (outside) the axis are colinear with K-12, and the segments below (inside) the axis are inverted relative to K-12. Since the difference in K-12 and 2457T genome lengths is small (0.8%) and large segments are homologous, the alignment between circles 7 and 8 is accurate within the limits of resolution for representation of the inversions. Blue represents colinear backbone, various shades of red represent backbone inverted in 2457T relative to K-12, various shades of green represent backbone translocated in 2457T relative to K-12, and yellow represents K-12- or 2457T-specific islands. Segments of the same color and length are homologous. The map was created by GenVision (DNASTAR).

Comparison of backbone proteins. E. coli K-12 proteins with orthologs in all four pathogens (S. flexneri, E. coli O157: H7, and S. enterica serovars Typhi and Typhimurium), were aligned with each pathogen ortholog, and the percentage of identity was calculated. The results are plotted as a histogram. White bars, S. flexneri; black bars, O157: H7; dark gray bars, S. enterica serovar Typhimurium; light gray bars, S. enterica serovar Typhi.

Diagram of the organization of ipaH genes in the 2457T and 301 genomes. Lines connect genes in the same positions relative to backbone. X marks genes inactivated by insertion sequences or frameshift mutations. Similar colors denote homology of the N-terminal portions of the encoded proteins. Asterisks show the relative positions of the terminus of chromosomal replication; a chromosomal rearrangement in 2457T spanning the terminus accounts for S1947 having the same flanking backbone regions as SF1383. The figure is not drawn to scale.

Venn diagram showing the distribution of common and unique ORFs among S. flexneri 2a, E. coli K-12, and E. coli O157: H7. Only complete protein-coding ORFs, including hypothetical unknowns, are included. The IS element and phage ORFs, as well as pseudogenes, are excluded.

Diagram of differences in genome organization between strains 2457T and 301. Diagonal lines join homologous regions that are not colinear in the two genomes. ter, terminus; ori, origin.