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Fig. S1 Schematic representation of the experimental procedure for transcriptome profiling of the rice response to As(III).

Fig. S2 Arsenic content in rice after As(III) treatment.

Fig. S3 Global patterns of 10 samples of gene expression.

Fig. S4 Number of differentially expressed genes (DEGs) modulated in response to As(III) treatments of varying times and dosages.

Fig. S5 Comparison of Illumina sequencing data and qRT-PCR results.

Table S1 List of primers used for qRT-PCR analysis

Table S2 Summary of mapping reads of the mRNA-seq

Table S3 List of 2081 differentially expressed genes (DEGs) both root and shoot samples

Table S4 List of differentially expressed genes (DEGs) encoding As transporter proteins

Table S5 KEGG pathways enriched in differentially expressed genes (DEGs)

Table S6 List of differentially expressed genes (DEGs) in JA biosynthesis and signaling pathways.

Table S7 List of differentially expressed genes (DEGs) in phytohormone biosynthesis and signaling pathways

Table S8 List of differentially expressed genes (DEGs) in lipid metabolism

Table S9 Summary of mapping reads of the miRNA-seq

Table S10 Expression profiling of miRNA and their target mRNA

Table S11 List of differentially expressed genes (DEGs) encoding rice transcription factors (TFs)

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