1. Figure S1. Effects of AVG, DIECA, DPI, NMMA, STA, and OKA on IbRPK expression in sweet potato (Ipomoea batatas cv. Tainung 57). Leaves with petiole cuts were immersed in water for 12 h, and then treated water, 0.88 mM AVG (a), 10 mM DIECA (a), 100 μM DPI (b), 500 μM NMMA (b), 1 μM STA (c), or 0.5 μM OKA (c) for another 12 h. Then, these leaves were unwounded (W-) or wounded (W+) by tweezers. The total RNAs of these leaves were analyzed by RT-PCR 0.5 h later. AVG is an ethylene biosynthesis inhibitor, DIECA is a JA biosynthesis inhibitor, DPI is a NADPH oxidase inhibitor, NMMA is a NOS inhibitor, STA is a protein kinase inhibitor, and OKA is a protein phosphatase inhibitor. The expression of IbActin in each assay was also analyzed by RT-PCR, and was treated as a loading control.

2. Figure S2. Secondary structure and sequence comparison of miR828 precursor. (a) Secondary structure of miR828 precursor was predicted by mfold (Zuker, 2003). The line indicates the position of the mature miR828. (b) Sequence comparison of miR828. Sequence comparisons were produced by MEGALIGN. Sequences identical are displayed as white letters in black boxes. Ib-premiR828 was compared with those encoding premiR828 in Arabidopsis thaliana, Arabidopsis lyrata, Salvia sclarea, and Vitis vinifera.

3. Figure S3. Putative conserved domains in IbRPK, IbTLD, and IbMYB. NCBI Conserved Domain Database (CDD) was used. (a) IbRPK contains Leucine rich repeat N- terminal domain and catalytic domain of protein kinase. (b) IbTLD contains TLDc domain. (c) IbMYB contains SANT domain.

4. Figure S4. The expression patterns of IbMYB-siRNA, IbTLD-siRNA, and miR828 in the leaves of wild type sweet potato (Ipomoea batatas cv. Tainung 57) upon wounding. The third fully expanded leaves were wounded by tweezers for 0 (W-), 0.5, 1, 3, and 6 h. The total RNAs from wounded leaves at the time indicated were analyzed by northern blotting for detecting miR828, IbMYB-siRNA (a), IbTLD-siRNA (b), and 5S rRNA. The values of miR828 and siRNA were adjusted by their corresponding amount of 5S rRNA for equality of loading. After the adjustment by 5S rRNA, the reaction with the unwounded leaves was treated as the normalized reference, with a value of one, for determining the relative amount of miR828 and siRNA.

5. Figure S5. Phylogenetic analyses of IbMYB and IbTLD. Phylogenetic trees were produced by MEGA 4.0 programs. (a) Phylogenetic analysis of IbMYB protein. IbMYB was compared with those encoding other R2R3-type MYB factors in Arabidopsis thaliana and Ipomoea batatas, which include AtMYB4 (NP_195574), AtMYB7 (NP_179263), AtMYB6 (NP_192684), AtMYB32 (NP_195225), AtMYB1 (NP_187534), AtMYB113 (NP_176811), AtMYB90 (NP_176813), AtMYB114 (NP_176812), AtMYB75 (NP_176057), and IbMYB1 (BAG68212). (b) Phylogenetic analysis of IbTLD protein. IbTLD was compared with those encoding similar proteins in various plant species, which include At4g39870 (NP_195697) from Arabidopsis thaliana, RCOM 0212730 (XP_002531255) from Ricinus communis, POPTRDRAFT 207435 (XM_002307051) and POPTRDRAFT 832269 (XM_002310528) from Populus trichocarpa, LOC100262287 (XM_002267254) from Vitis vinifera, and Os02g0754000 (NP_001048151) and Os06g0221100 (NP_001057175) from Oryza sativa.

6. Figure S6. Protein sequence comparisons of miR828 targets, IbMYB and IbTLD.

7. Figure S6. Protein sequence comparisons of miR828 targets, IbMYB and IbTLD. (continued) Protein sequence comparisons were produced by MEGALIGN. Amino acid residues identical to those in target proteins are displayed as white letters in black boxes. (a) IbMYB was compared with those encoding R2R3-type MYB factors in Arabidopsis thaliana and Ipomoea batatas, which include AtMYB4 (NP_195574), AtMYB7 (NP_179263), AtMYB6 (NP_192684), AtMYB32 (NP_195225), AtMYB1 (NP_187534), AtMYB113 (NP_176811), AtMYB90 (NP_176813), AtMYB114 (NP_176812), AtMYB75 (NP_176057), and IbMYB1 (BAG68212). (b) IbTLD was compared with those encoding similar proteins in various plant species, which include At2g05590 (NP_849938) and At4g39870 (NP_195697) from Arabidopsis thaliana, RCOM 0212730 (XP_002531255) from Ricinus communis, POPTRDRAFT 207435 (XM_002307051) and POPTRDRAFT 832269 (XM_002310528) from Populus trichocarpa; LOC100262287 (XM_002267254) from Vitis vinifera; and Os02g0754000 (NP_001048151) and Os06g0221100 (NP_001057175) from Oryza sativa.

8. Figure S7. The expression patterns of the phenylpropanoid pathway genes and antioxidant enzyme genes in transgenic tobacco (Nicotiana tabacum L. cv. W38) overexpressing IbMYB and IbTLD. The total RNAs from Wild-Type (W38) and transgenics overexpressing IbMYB (IbMYB-1 and IbMYB-2) or IbTLD (IbTLD-1 and IbTLD-2) were used to detect the phenylpropanoid pathway genes, antioxidant enzyme genes, and NtActin expression using quantitative RT- PCR. The expression levels of NtActin were used as controls for quantitative comparison.