Extended Data Fig. 5: Genome-wide gene expression profiling of ETIAvrRps4.
From: Mutual potentiation of plant immunity by cell-surface and intracellular receptors
a, Schematic design of RNA-seq analysis. Five-week-old inducible lines of wild-type AvrRps4 (Est:AvrRps4) and mutant AvrRps4 (oestradiol-inducible AvrRps4KRVY135–138AAAA-expressing line; Est:AvrRps4mut) were infiltrated with mock or 50 μM oestradiol and samples were collected at 0 and 4 h. Samples from three biological replicates were collected for RNA-seq analysis. b, A total of 2,573 differentially expressed (DE) genes were identified as significant in a comparison between Est:AvrRps4 treated with oestradiol for 0 h (Est:AvrRps4 (Est-0h)) and Est:AvrRps4 treated with oestradiol for 4 h (Est:AvrRps4 (Est-4h)). P values for differentially expressed genes were generated with Fisher Z-transformation after Student’s t-test. Differentially expressed genes with a two-sided adjusted P value < 0.01 (adjusted by Benjamini and Hochberg’s false discovery rate (FDR) method) are categorized as significant. Heat map represents the 2,573 differentially expressed genes during five treatments: Est:AvrRps4 (untreated), Est:AvrRps4 treated with oestradiol for 0 h (Est-0h), Est:AvrRps4 treated with oestradiol for 4 h (Est-4h), Est:AvrRps4mut treated with oestradiol for 0 h (Est-0h) and Est:AvrRps4mut treated with oestradiol for 4 h (Est-4h). Genes that are specifically upregulated during ETIAvrRps4 are in clusters 7 and 8. c–e, Gene ontology (GO) enrichment analysis of genes from clusters 7 and 8. c, Top three significantly enriched biological process GO terms in clusters 7 and 8. d, Top four significantly enriched molecular function GO terms in clusters 7 and 8. e, Top four significantly enriched cellular component GO terms in clusters 7 and 8. For details of GO enrichment analysis refer to the relevant Source Data. f, Red (positive log2-transformed fold change) represents genes that are significantly induced and blue (negative log2-transformed fold change) represents genes that are significantly repressed. Data represent log2-transformed fold changes in gene expression (normalized against expression of the corresponding genes before ETIAvrRps4 activation). Benjamini–Hochberg FDR two-sided adjusted P value (adj.pval) < 0.05 is considered as significant. Gradient of green colour indicates significance of the adjusted P value. For a full list of differentially expressed genes refer to Supplementary Table 4.
