Supplement 1 PCA analysis of metabolite data from untreated rice genotypes by LC-TOF and GC-TOF mass spectrometry. Top panel: (A) LC-TOF analysis of Xa21.

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Supplement 1 PCA analysis of metabolite data from untreated rice genotypes by LC-TOF and GC-TOF mass spectrometry. Top panel: (A) LC-TOF analysis of Xa21 (black solid circles) and TP309 (gray solid circles) extracts in negative electrospray ionization using 80 masses that were constrained by a 100% class frequency 870 threshold, i.e. presence in 6 out of 6 biological replicates in at least one group. Bottom panel: (B) GC-TOF analysis of Xa21 and TP309 extracts using 441 metabolites constrained by a 50% class frequency threshold A B

Supplement table S2. List of all 441 metabolites positively detected by GC-TOF and ChromaTOF/BinBase data processing in at least 50% of the samples in at least one study design class. Each metabolite is assigned by full analytical-chemistry metadata and database identifiers. For each compound, p-values and intensity ratios are given for pair-wise comparisons. ….

Supplement S3. ANOVA for LC-TOF data comparing the three Xa21 conditions. Using the Tukey one-way post-hoc test, the total number of statistically significant masses are given in grey blocks, with the number of statistically significant different features (p<0.05) given in red blocks and the numbers of non- different features given in blues boxes. (A) LC TOF mass spectrometry in positive ionization mode (B ) LC TOF mass spectrometry in negative ionization mode

Supplement table S4. Differentially expressed metabolites in pair-wise comparisons analyzed by LC-TOF MS in positive and negative ion modes for compounds having both greater than 2-fold change and p<0.05. Metabolites were annotated using the METLIN personal metabolite database for a mass match (mass delta window < 5 ppm).

Supplement S5. Analysis of Rice RNA integrity measured by the Agilent 2100 Bioanalyzer. Agilent 2100 biosizing software displays electropherogram images of total RNA samples, one representative per group, extracted from rice leaves subsequent to metabolite extractions. (A)Xa21_PXO99 (B)Xa21_NT (C)Xa21_Mock (D)Xa21_raxST- (E)TP309_PXO99 (F)TP309_NT (G)TP309_Mock.

Supplemental S6. Table of selected significantly differentially expressed genes for three conditions: Xa21_PXO99/Mock, Xa21_PXO99-raxST-/Mock, and TP309_PXO99/Mock. All ratios are expressed relative to mock infection.