Rooted phylogenies for T3SS genes <i>escV, escN, escF,</i> and <i>escJ</i>. BI trees for the four T3SS genes described in Castillo et al., [<b>12</b>] are depicted with long branches truncated (//) and the total branch length indicated above.

<p>The subtree in the box represents BI branching on a different scale from the larger trees. Taxa are colored by presence in the clades described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0041615#pone-0041615-g003" target="_blank">Figure 3</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0041615#pone-0041615-g005" target="_blank">5</a> to facilitate comparison between trees (clade I – purple, clade II – green, clade III – blue, clade IV – orange, clade V – red). Taxa enclosed by braces had identical sequences to the adjacent taxa and were therefore removed from the phylogenetic analysis. Diversity values (è) below gene names are calculated excluding the outgroup and those calculations also excluding the SESS LEE genes are in parentheses. Numerals at tree junctions are the percentage posterior probability.</p

Genes in the SESS LEE genomic island.

a<p>Gene names modified from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0041615#pone-0041615-t001" target="_blank">Table 1</a> in Pallen et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0041615#pone.0041615-Pallen1" target="_blank">[11]</a> with alternative names.</p>b<p>Product names derived from annotation of SESS1296 and modified from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0041615#pone-0041615-t001" target="_blank">Table 1</a> in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0041615#pone.0041615-Pallen1" target="_blank">[11]</a>.</p>c<p>Structural components of the T3SS are indicated with (+).</p>d<p>Diversity (θ) for the listed LEE gene from all alignments including the two <i>Salmonella</i> LEE with standard deviations listed in parentheses.</p>e<p>Diversity (θ) for the listed LEE gene from all alignments excluding the two <i>Salmonella</i> LEE with standard deviations listed in parentheses.</p>f<p><i>Salmonella</i> variants of LEE genes with “orf” designations utilize locus tags as gene names.</p

Phylograms of the consensus BI tree for the matrix of LEE T3SS genes.

<p>All diagrams are presented with long branches truncated (//) and the branch length indicated above. The subtree in the box represents BI branching on a different scale from the larger tree. Taxa are colored based upon the tRNA insertion point with <i>selC</i> in red, <i>pheV</i> in blue, <i>pheU</i> in green, and black for all other insertion points. Clades are indicated by large Roman numerals above calculated level of genetic diversity (θ) for all the members of the clade. The BI tree is midpoint rooted with posterior probability values represented as a percentage at branch points. ML analysis yielded the same branching (although differential branch lengths) and ML percentage bootstrap values are presented in parentheses () when this value differed from the percent posterior probability. Taxa enclosed by braces had identical sequences to the adjacent taxa and were therefore removed from the phylogenetic analysis.</p

Schematic of the genomic island containing LEE.

<p>The extent of the genomic island is marked by the solid gray line and the bounding genomic genes outside the genomic island are marked in yellow. Genes that are not part of the LEE region are marked in grey. Genes that form the T3SS are shown in green, the <i>pheV</i> tRNA insertion point is marked by a small red arrow with the remainder of the LEE region in blue. Redundant text from the locus tags has been removed to simplify the figure. The full locus tag of those genes designated with a 4 digit number would read SESS1296_0XXXX. The operon structure of the LEE region is indicated by black arrows. Gene functions are abbreviated, putative integrase (INT), putative transcriptional regulator (TR), putative secreted effector (SE). Groups of genes for which homologs co-occur in other organisms are indicated by curly brackets. Possible pseudogenes are marked with (*). G+C content calculated with a 100 bp window is depicted by the graph below the diagram with maximum (upper line = 61%) and minimum (lower line = 24%) values designated. Typical G+C content of 52% for <i>Salmonella</i> genomes is depicted by the dashed red line. Four tandem repeat regions are depicted by small red boxes. A plot of genetic diversity (θ) calculated for each LEE gene using a Watterson estimate is represented as a spot below the relevant gene.</p

LEE and non-LEE containing strains used in this study.

a<p>Completed or draft genome sequence available and used for housekeeping gene phylogeny.</p>b<p><i>E. coli</i> STEC O157:H7 str. Sakai is the representative strain for the other <i>E. coli</i> O157 LEE.</p>c<p>Corrected likely sequence error that caused a frame shift mutation by deleting a C at position 208 in the CDS encoding <i>cesA.</i></p

Results of statistical tests for recombination.

a<p>P-value calculated with permutation test (5000 iterations).</p>b<p>Window size was set to 100.</p>c<p><i>Salmonella</i> sequences removed from alignments prior to calculation.</p

A 95% majority rule tree estimated for the T3SS genes with ClonalFrame allowing the program to determine the effect of recombination (A) or fixing the recombination rate at zero (B).

<p>Clades numbered I-V are indicated next to respective taxa. Taxa are colored based upon the tRNA insertion point with <i>selC</i> in red, <i>pheV</i> in blue, <i>pheU</i> in green, and black for all other insertion points. The scale is time in coalescent units.</p

Comparison of the operon arrangements between SESS LEE and <i>E. coli</i> LEE.

<p>Core LEE genes from <i>E. coli</i> O157:H7 Sakai and <i>Salmonella</i> are connected by lines indicative of segments that match in a tblastx comparison. Genes and arrows indicating the extent of the LEE operons are colored to facilitate comparison. Genes outside the operons are colored gray and those genes present in <i>E. coli</i> but absent in <i>Salmonella</i> are colored red. Filled arrows are drawn to scale and accurately positioned based on the genome sequences they depict.</p