Figure 3. Analysis of plasmid variation reveals multiple patterns in distribution.

Rows indicate genes present in (blue) or absent from (white) the plasmids of isolates (listed to the right; D188 is labeled in red for reference). Columns represent individual genes. Type categories were determined on the basis of phylogenetic analysis of the core genes. INDEL variants, delineated by gray and white shading, were determined on the basis of the cladogram. The plasmid carried by LMG3616 is enclosed by dotted lines. The lower-case letters and numbers (a1, a2, b, c1, and c2) listed along the right, relate isolates and their plasmids to the potential transmission patterns indicated in Figure 2.

Figure 3—figure supplement 1. Presence/absence-cladogram and phylogeny support the classification scheme for the virulence plasmid.

The dashed lines show congruency in results from methods used to cluster plasmid types; (left) plasmids were clustered in a cladogram on the basis of the presence/absence of genes and (right) in a phylogenetic tree on the basis of the concatenated sequences of 123 genes that are present in more than 95% of the virulence plasmid sequences. Red and green blocks delineate Type I and Type II plasmids, respectively.

Figure 3—figure supplement 2. Both types of virulence plasmids are present in both clades of pathogenic Rhodococcus.

The multilocus sequence analysis (MLSA) phylogenetic tree of the four plant-associated clades was associated with the phylogenetic tree on the basis of the concatenated sequences of 123 genes that are present in more than 95% of the virulence plasmid sequences. The lines between trees show relationships between isolates and plasmids. The two pairs of solid (black and red) lines highlight examples of closely related isolates that have divergent plasmid types and distantly- related isolates that have similar plasmid types.