Fig. 1. The pathogenic clade of P. viridiflava ATUE5 harbors a single highly conserved viral cluster (VC2).

(A) Maximum likelihood concatenated core genome phylogeny of 1524 pseudomonads that co-occur in the A. thaliana phyllosphere (light blue bar). The dark blue bar indicates a pathogenic clade of P. viridiflava ATUE5 [adapted from Karasov et al. (2)]. (B) Frequency of viral elements identified in each Pseudomonas genome. Each genome harbors between one and eight viral elements. (C) Principal component analysis of viral elements based on pairwise k-mer Mash distances (27) and silhouette analysis reveals four defined clusters. Points are colored as indicated in the inset. (D) Viral elements of VC2 are present in all genomes of the pathogenic operational taxonomic unit (OTU) ATUE5. The phylogeny shows the relationships among 1524 Pseudomonas strains. Each stacked bar around the phylogeny indicates the presence of a viral element (with a maximum height of eight viral elements). The bars are colored as in (C). The outer circle shows strains that belong to ATUE5 (green) and other OTUs (black).