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.

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.

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.

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.

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.

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

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.

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.