Fig. 2

Significantly differentially expressed genes between ‘Control’ and ‘LAP1’ agroinfiltration conditions. a Scatter plot showing the correlation for significantly differentially expressed genes between Control (x-axis) and LAP1 (y-axis) replicate sets (Pearson correlation value = 0.983). Differential expression analysis between the two replicate sets was performed on raw counts with annotated mRNAs via the DESeq2 Filter [35] and combined with the Intensity Difference Filter using SeqMonk [62] (see “Methods”). mRNAs were considered significantly differentially expressed when the adjusted P value was <0.05 (blue dots). Grey dots represent all other mRNAs in the M. truncatula genome (version Mt4.0), showing the relationship between the quantitated values in the Control and LAP1 replicate sets. b Hierarchical clustering of differentially expressed genes between ‘Control’ and ‘LAP1’ agroinfiltration conditions. With a correlation coefficient of 0.7, 109 genes fell in to 8 clusters with three major categories: low-moderate expression in control conditions, moderate induction by MtLAP1 infiltration (cluster 1); very low expression in control conditions, induced by MtLAP1 infiltration (cluster 2); moderate expression in control conditions, highly induced in response to MtLAP1 infiltration (cluster 3). Values are log₂-transformed library-normalized/median-normalized counts