Contrasting Potato Foliage and Tuber Defense Mechanisms against the Late Blight Pathogen Phytophthora infestans
Fig 5
Hierarchical clustering of shared (foliage and tuber) DE genes.
Foliage and tubers of nontransformed ‘Russet Burbank’ (WT) and transgenic SP2211 (+RB) were inoculated with P. infestans or water. Tuber samples collected at 0, 24, 48 hpi and foliage samples collected 0, 6, and 24 hpi were subjected to RNA-seq, revealing a total of 1,102 (for tubers) [8] and 475 (for foliage) DE genes between water- and P. infestans-inoculated comparisons within the same genotype and the same time point. A total of 127 DE genes are shared between both foliage (FDR<0.01) and tubers (FDR< = 0.001). Log2(FPKM_p.inf/FPKM_mock) values were used to cluster these 127 DE genes in Cluster 3.0 [20] as described in detail previously [8]. Results were visualized using Treeview [20]. Red indicates genes that are up-regulated, green indicates genes that are down-regulated. (A) Global visualization of the 127 DE genes; (B) a small cluster of photosynthesis genes down-regulated in all tissues; (C) A small gene cluster harboring carbonic anhydrase (CA); (D) a small cluster representing genes that are generally up-regulated under all conditions. (E-F) Small clusters of DE genes showing higher induction in +RB in both foliage (at 24 hpi) and tubers (at 48 hpi).