Supplemental Information
Fig. S1 Expression patterns of Xanthomonas oryzae pv. oryzae (Xoo) genes in six libraries (H471-
1d, H471-3d, HHZ-1d, HHZ-3d, P28-1d and P28-3d). (A) The venn diagram showing the distribution of expressed Xoo unigenes among libraries H471-1d, HHZ-1d and P28-1d. (B) The venn diagram showing the distribution of expressed Xoo unigenes among libraries H471-3d,
HHZ-3d, and P28-3d. (C) Clustering of total expressed Xoo genes.
Fig. S2 Expression patterns of rice genes in six libraries (H471-1d, H471-3d, HHZ-1d, HHZ-3d,
P28-1d and P28-3d). (A) Clustering of the total expressed rice genes. (B) The venn diagram showing the distribution of expressed rice unigenes among libraries H471-1d, HHZ-1d and
P28-1d. (C) The venn diagram showing the distribution of expressed rice unigenes among libraries H471-3d, HHZ-3d, and P28-3d.
Fig. S3 The correlation between the transcription measurements by Illumina sequencing and those qRT-PCR assays.
Fig. S4 GO terms of differentially expressed genes (DEGs) of Xanthomonas oryzae pv. oryzae
(Xoo) in H471 when compared with those in its parents, HHZ and P28. (A) H471-1d vs HHZ-
1d. (B) H471-1d vs P28-1d. (C) H471-3d vs HHZ-3d. (D) H471-3d vs P28-3d.
Fig. S5 GO terms of differentially expressed genes (DEGs) of rice in H471 compared with its parents, HHZ and P28. (A) Common between the incompatible interaction (H471) and compatible ones (HHZ and P28) at 1 dpi and 3 dpi. (B) The specific GO terms of the DEGs in
H471 when compared with both parents at 1 dpi. (C) The specific GO terms of the DEGs in
H471 when compared with its parents (HHZ and P28) at 3 dpi.
Fig. S6 Hierarchical clustering of differentially expressed rice protein kinases in H471 infected by Xanthomonas oryzae pv. oryzae (Xoo) isolate POX99. The color scale indicates the gene expression value (light blue indicates hi g her expression values, dark blue indicates lower gene expression values). The raw data represented here are detailed in S10, see Supporting
Information. Colored bars on the left of the heatmap mark significant differences between

H471 and its parents, in which magenta and cyan indicate up-regulated and down-regulated genes in H471 when compared with HHZ; orange and green indicate up-regulated and downregulated genes in H471 when compared with P28; red and blue indicates up-regulated and down-regulated genes in H471 when compared with HHZ and P28; and black indicates genes with the opposite expression trend in H471 when compared with HHZ and P28.
Fig. S7 Differentially expressed genes (DEGs) of rice encoding TFs in H471 compared with its parents. (A) Venn diagram showing the distribution of differentially expressed rice TFs. (B)
Hierarchical clustering of differentially expressed TFs infection in H471 infected by
Xanthomonas oryzae pv. oryzae (Xoo). The raw data represented here are detailed in Table
S11, see Supporting Information. Colored bars on the left of the heatmap mark significant differences between H471 and its parents, in which magenta and cyan indicate up-regulated and down-regulated genes in H471 when compared with HHZ; orange and green indicate upregulated and down-regulated genes in H471 when compared with P28; red and blue indicates up-regulated and down-regulated genes in H471 when compared with HHZ and
P28; and black indicates genes with the opposite expression trend in H471 when compared with HHZ and P28.
Fig. S8 The numbers of important Xanthomonas oryzae pv. oryzae (Xoo) genes and rice genes which were specifically expressed or up-regulated in the incompatible interactions between
PXO99 and H471 at 1 and 3 dpi when compared with the compatible interactions of both or either parent. (A) Xoo genes, the raw data represented here are detailed in Table S17, see
Supporting Information. (B) Rice genes, the raw data represented here are detailed in Table
S18, see Supporting Information. Where I: H471 vs HHZ and P28, II: H471 vs HHZ, and III:
H471 vs P28, and * represents 3 genes which exhibited the opposite expression trends between 1 dpi and 3 dpi. The full and open shapes indicate the genes were up-regulated and down-regulated in H471 compared with HHZ and P28 after Xoo inoculation, respectively.
Table S1 Average lesion lengths (in cm) of HHZ, P28 and H471 caused by 14 Philippines
Xanthomonas oryzae pv. oryzae (Xoo) races and a Chinese Xoo race (C5) measured 2 weeks after inoculation.

Table S2 Expression levels of the Xanthomonas oryzae pv. oryzae (Xoo) unigenes in the two incompatible (H471-1d and H471-3d) and 4 compatible (HHZ-1d, P28-1d, HHZ-3d and P28-
3d) rice libraries detected by RNA-seq.
Table S3 Expressed rice unigenes in the two incompatible (H471-1d and H471-3d) and 4 compatible (HHZ-1d, P28-1d, HHZ-3d and P28-3d) rice libraries detected by RNA-seq.
Table S4 The primer sequences used for qRT-PCR analyses of 35 rice DEGs and 11 Xanthomonas
oryzae pv. oryzae (Xoo) differentially expressed genes (DEGs).
Table S5 Summary of differentially expressed genes (DEGs) of Xanthomonas oryzae pv. oryzae
(Xoo) in the incompatible (H471-1d and H471-3d) and compatible interactions (HHZ-1d, P28-
1d, HHZ-3d and P28-3d).
Table S6 Differentially expressed genes (DEGs) of Xanthomonas oryzae pv. oryzae (Xoo) in the incompatible (H471-1d and H471-3d) and compatible interactions (HHZ-1d, P28-1d, HHZ-3d and P28-3d).
Table S7 Summary of differentially expressed genes (DEGs) of rice in the incompatible (H471-1d and H471-3d) and compatible interactions (HHZ-1d, P28-1d, HHZ-3d and P28-3d).
Table S8 Differentially expressed genes (DEGs) of rice in the incompatible (H471-1d and H471-
3d) and compatible interactions (HHZ-1d, P28-1d, HHZ-3d and P28-3d).
Table S9 Differentially expressed genes (DEGs) of rice encoding response regulator receivers in
H471 compared with HHZ and P28 at 1 dpi.

Table S10 Differential expression of rice protein kinases and protein phosphatases 2C in H471 compared with HHZ and P28.
Table S11 Differentially expressed genes (DEGs) of rice encoding TFs and histone proteins in the incompatible interactions of H471 when compared with the compatible ones in HHZ and P28.
Table S12 Differentially expressed genes (DEGs) of rice encoding pentatricopeptide repeat
(PPR) and tetratricopeptide repeat (TPR)-like superfamily protein in H471 compared with
HHZ and P28.
Table S13 Differential expression of rice resistance genes in H471 infected by Xanthomonas
oryzae pv. oryzae (Xoo) compared with its parents.
Table S14 Rice genes in co-regulatory networks in response to infection by Xanthomonas
oryzae pv. oryzae (Xoo) based on the Rice Oligonucleotide Array Database.
Table S15 The expression levels of the representative PRRs and genes related to the cell death due to ion fluxes and ROS in H471 compared with parents after inoculation with
Xanthomonas oryzae pv. oryzae (Xoo).
Table S16 The expression levels of Ax21 and related genes between compatible interactions an incompatible interaction.
Table S17 List of important differentially expressed Xanthomonas oryzae pv. oryzae (Xoo) genes detected in the comparison between the incompatible interactions of H471 and the compatible ones, HHZ and P28 inoculated by Xoo race, PXO99.

Table S18 List of important differentially expressed rice genes detected in the comparison between the incompatible interactions of H471 and the compatible ones, HHZ and P28 inoculated by Xanthomonas oryzae pv. oryzae (Xoo) race, PXO99.