Fig. 4From: Long-term effect of epigenetic modification in plant–microbe interactions: modification of DNA methylation induced by plant growth-promoting bacteria mediates promotion processChanges in gene expression profiles in roots induced by the rhizosphere microbiome. A Venn diagram of DEGs in inoculated samples in the early and late phases. The DEGs were identified by comparisons of non-inoculated (CK) vs. inoculated (PGP5/PGP41) samples (FDR < 0.05; fold change ≥ 2). B WGCNA showing significant correlation between module eigengenes (ME) and traits of the rhizosphere microbiome represented by PCoA1–3 in Fig. 1G. Each module corresponds to a distinct color shown in the left color column; correlation coefficients are shown in the right color bar. The numbers in cells refer to the correlation coefficient and the corresponding P value (numbers in brackets) between modules traits. C A scatterplot of gene significance (GS) versus module membership (MM) in the most significant module (turquoise module), with a correlation coefficient of 0.81 and P < 2e–200Back to article page