Repeated extragenic palindromic (REP) elements and REP–associated tyrosine transposases (RAYTs) of the <i>P. fluorescens</i> group.

<p>The left panel shows a phylogenetic tree, generated using the MrBayes package <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002784#pgen.1002784-Ronquist1" target="_blank">[152]</a>, depicting the relationships between RAYT proteins identified within each strain of the <i>P. fluorescens</i> group. The interior node values of the tree are clade credibility values, which represent the likelihood of the clade existing, based on the posterior probability values produced by MrBayes. The locus tags for primary RAYT proteins are shaded according to sub-clade using the color scheme of <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002784#pgen-1002784-g001" target="_blank">Figure 1</a>; locus tags for secondary RAYT proteins are not shaded. The second primary RAYT in Q8r1-96 is within PflQ8_0107, in a separate reading frame. The right panel shows schematic representations of the RAYT genes (dark blue arrows) and the locations of associated flanking REP elements (REPa sequences in grey; REPd in orange; and REPe in light blue). The <i>P. aeruginosa</i> RAYT protein encoded by PA1154 is used as an outgroup, since this RAYT protein was shown previously to fall within a clade separate from the <i>P. fluorescens</i> RAYT proteins <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002784#pgen.1002784-Bertels1" target="_blank">[44]</a>.