Fig. 1
Transcriptomic profile of R. solanacearum UY031 in planta. a. Shared and unique DE genes across the three in planta conditions for the up-regulated (left) and down-regulated (right) genes. Each vertical bar plot represents the number of shared DE between the conditions indicated by the lines and dots in the schematic below. The horizontal bar plots on the right indicate the total DE genes per in planta condition compared to rich medium. b. For the intersection of Apoplast, Early and Late (in planta genetic programme), Early and Late (Xylem genetic programme), Apoplast and Late xylem alone, the list of genes was extracted and surveyed for enriched KEGG pathways. Dot plots of the enriched KEGG pathways for the up- (left) and down-regulated (right) genes in each environment are shown below. DE genes were identified with DEseq2 (p-adj > 0.01, log2 FC ± 1.5) and plotted using the R package UpsetR