Fig. 1

Overview of study. A Medicago roots were subjected to LCO treatment, followed by time course profiling of ATAC-seq and RNA-seq measurements. The data were analyzed using computational tools for differential gene expression analysis (DE analysis), time course gene expression analysis (ESCAROLE), and integrative analysis of RNA-seq and ATAC-seq time course (DRMN). Outputs from these tools were used to find gene modules, transitioning genes, TF-target interactions, and prioritize regulators. B Principal component analysis (PCA) of expression time course showing grouping and ordering of the (3) biological replicates per time point. Principal components 1, 2, and 3 explain ~50% of the variation. C Similarity scores (F-score) between the differentially expressed genes (DEG) set obtained in this study (LCO treatment) and DEG sets identified from previously published time-course data under rhizobium treatment from Larrainzar et al. For the latter data, DEGs were called with respect to control for each time course (rows and columns corresponding to WT, nfp, lyk3, skl) and with respect to WT at each time point for each mutant strain (rows and columns with “vs. WT” labels). D Expression patterns of known nodulation and symbiosis genes (NIN, CRE1, ENOD11, RPG, and ERN1) in our dataset (LCO treatment) and in the four rhizobia treatment time courses from Larrainzar et al. (WT, nfp, lyk3, skl). The systematic names for the shown genes are MtrunA17Chr5g0448621 (NIN), MtrunA17Chr8g0392301 (CRE1), MtrunA17Chr3g0082991 (ENOD11), MtrunA17Chr1g0197491 (RPG), and MtrunA17Chr7g0253421 (RPG)