Figure 2.

Phylogenetic relationships based on housekeeping genes vs. TAL effectors, and whole genome alignments of the Xoc strains. (A) Maximum likelihood trees, created using concatenated alignments of the nucleotide sequences of either 31 housekeeping genes or the TAL effectors in each of the 39 ortholog groups shown in Figure 1. Bootstrap values from 1000 replicates are given at the nodes. (B) Alignment of the whole genome of every strain, generated using progressiveMauve (Darling et al., 2010). Colored blocks represent regions of uninterrupted homology, connected between genomes by matching colored lines. The height of the colored bars within each block indicates relative conservation on average across all genomes. Homologous regions above the centerline are in the same orientation as they are in BLS256 and those below are inverted.