Figure 5. Strains of phylogenetic group II have the fewest non-effector genes in their HrpL regulons.

“Non-effector” genes are listed across the top; Pseudomonas genomes, color-coded by phylogenetic group, on the left, according to Figure S5 (Pseudomonas UB246 was not included, because it belongs to a divergent pseudomonad lineage). Only the first gene of an operon is represented. Dark blue box indicates presence of full-length ORFs (with at least 80% nucleotide identity and 40% coverage), by similarity search as well as the presence of a hrp-box in the 500 bp upstream region. Grey boxes indicate that the corresponding gene was present, but the presence of putative hrp-boxes could not be determined, due to incomplete sequencing of the upstream region. Yellow boxes indicate that genes are present but either no hrp-boxes were detected in the upstream region or hrp-boxes are presumably not functional (because divergent from the hrp-box for which HrpL-dependent expression was confirmed). White boxes indicate absence of genes based on homology searches. The light blue boxes indicate the presence of a divergent ORF with upstream hrp-box sequence present. S, indicates that the gene is present as a single gene. O, indicates that the gene is present in an operon. + or − indicate that the gene was differentially expressed or not in our RNA-seq data. ND indicates not determined: PSPTO_A00030 is absent from our Pto _DC3000 laboratory strain, and a homologous sequence of Psyr_0737 is present in Pja genome but was not annotated as an ORF.