Figure 5

Hierarchical clustering of differentially expressed (DE) genes in potato tubers following inoculation with Phytophthora infestans. Tubers of nontransformed ‘Russet Burbank’ (WT) and transgenic SP2211 (+RB) were inoculated with P. infestans or water. Tuber samples collected 0, 24, and 48 hpi were subjected to RNA-seq, revealing a total of 1,102 DE genes between water- and P. infestans-inoculated comparisons within the same genotype and the same time. Log2(FPKM_p.inf/FPKM_mock) values were used to cluster 1,102 DE genes (FDR<0.001) in Cluster 3.0 [51] using uncentered correlation and the complete linkage method. Results were visualized using Treeview [51]. (A) Global visualization of the 1,102 DE genes; (B) A small gene cluster differentially regulated in +RB and WT at 24 and 48 hpi; (C) A small gene cluster differentially regulated in +RB and WT only at 48 hpi. Red indicates genes that are up-regulated, green indicates genes that are down-regulated.