Related to Figures 4A, S5A, and S5B; see also Data S1, S2B, and S2C. Heatmaps of all DEGs in WT, lsh1, lsh1/lsh2, and noot1/noot2 at 24 and 72 hpi. Expression levels are depicted as log2fold changes ≥ ±0.585 (raw fold change of 1.5), p < 0.05. LSH1 DNA-binding sites associated with rhizobial-responsive DEGs are depicted in dark green: high confidence, light green: moderate confidence, or gray: low/no confidence. To compare the overall transcriptional response to S. meliloti spot inoculation between WT and the mutants, we sorted all DEGs from the highest positive to the highest negative log2fold change values. Absolute numbers indicate responsive DEGs, and percentages indicate the proportion of DEGs in WT that are not differentially expressed in the mutants and therefore affected by loss of LSH1, LSH1/LSH2, and NOOT1/NOOT2.
