Fig. 5

WGCNA analysis of 8 B. xylophilus transcriptomes (all figures were generated by the authors of this study). a. Analysis of network topology for various soft-thresholding powers. The left panel shows the scale-free fit index (y-axis) as a function of the soft-thresholding power (x-axis). The right panel displays the mean connectivity (degree, y-axis) as a function of the soft-thresholding power (x-axis). b. Clustering dendrograms of genes with dissimilarity based on the topological overlap, together with assigned module colors. As a result, 25 coexpression modules were constructed and are shown in different colors. c. Visualizing the gene network using a heatmap plot. The heatmap depicts the topological overlap matrix among all genes in the analysis. Light color represents low overlap, and the progressively darker red color indicates increased overlap. Blocks of darker colors along the diagonal are the modules. The gene dendrogram and module assignment are also shown along the left side and the top. d. 1: CK2, 2: nematodes induced by P. massoniana for 1 day, 3: nematodes induced by P. massoniana for 15 days, 4: nematodes induced by P. sylvestris var. mongolica for 15 days, 5: nematodes induced by P. thunbergii for 1 day, 6: nematodes induced by P. thunbergii for 15 days, 7: Treatment 1, 8: CK1