Variable Suites of Non-effector Genes Are Co-regulated in the Type III Secretion Virulence Regulon across the Pseudomonas syringae Phylogeny
Figure 1
Validation of our RNA-seq method.
(A) Read coverage of PtoDC3000 genes within and between biological replicates displays high reproducibility. A graphical logarithmic representation of the median read counts of all genes covered by unique reads after bootstrapping of the data is presented. Top panels: comparison of PtoDC3000(pBAD::hrpL) and PtoDC3000(pBAD::EV) samples within (left) the first (HrpL1 or EV1), or the second (HrpL2 or EV2) (right) biological replicate. Bottom panels: comparison of PtoDC3000(pBAD::EV) samples (left), and PtoDC3000(pBAD::hrpL) samples (right) across two biological replicates. Red dots represent the logarithmic median read count of genes found to be significantly up-regulated in the presence of HrpL by GENE-counter with a B-value≥50%. (B) Graphical representation of GENE-counter data for PtoDC3000 bootstrapped 300 times. Genes identified as differentially up-regulated were plotted according to their Log (Median q-value). Data points were color-coded for putatively novel genes (genes not previously described as HrpL-regulated, in red), genes previously described as HrpL-regulated, hrp complex genes, type III effector genes (in black), and genes involved in coronatine synthesis (in yellow). avrE is marked in blue. (C) Draft and complete (NCBI) PtoDC3000 reference genomes yield highly similar RNA-seq results. Every gene found up-regulated with a B-value≥50 using both NCBI and draft genome as reference genomes was plotted according to its Log (median q-value).
