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Table S12. Primers used in this study. (DOCX 2617Â kb)

Table S10. Legumain-like Cysteine Proteases in four plant species. (DOCX 16Â kb)

Figure S2. Multiple protein sequences alignment of rice legumain-like cysteine proteases. The peptidase C13 domain was shaded. The similar amino acid residues were marked in blue and the identical acid residues were boxed in purple. Red dots indicate the catalytic triad. (DOCX 481Â kb)

Figure S6. Expression profile of OsCPs in the shoots and roots under different plant hormones treatments. (DOCX 482Â kb)

Table S4. Expression abundance of OsCPs and OsVPEs in various tissues under normal conditions. (DOCX 20Â kb)

Table S9. Papain-like Cysteine Proteases in three plant species. (DOCX 18Â kb)

Figure S11. Expression profile of OsVPEs in the shoots and roots under different plant hormones treatments. (DOCX 214Â kb)

Figure S5. Expression heatmap of OsVPEs in different tissues under normal conditions. (DOCX 263Â kb)

Table S7. Expression change of OsCPs and OsVPEs under stress treatments. The date was from MPSS: gene analysis ( http://mpss.udel.edu/rice/GeneQuery.php ). The experiment materials were 14-day-old seedlings. Salt treatment: 250 mM NACL for 24 h; drought treatment: stressed in drought for 5d; cold treatment: 4 °C for 24 h. Compared with normal condition, the expression fold change > 2 or

Figure S1. Multiple protein sequences alignment of rice papain-like cysteine proteases. The inhibitor domain and peptidase C1A domain was shaded in red and black respectively. The granulin domain was marked with black boxes. The similar amino acid residues were marked in blue and the identical acid residues were boxed in purple. Red and black dots indicated the catalytic triad and the retention signal in ER respectively. The â NPIRâ was shaded in a black ellipse. (DOCX 868Â kb)

Table S8. Overview of cis-elements in the promoters of OsCPs and OsVPEs. ABRE: ABA-responsive element; LTRE: Low-temperature-responsive element; DRE: Dethydration-responsive-element; T/G-box: DNA-binding motif of MYC2 (the key transcriptional activator of jasmonate responses). The number of predicted cis-elements were presented by the number of â +â . (DOCX 17Â kb)

Figure S3. Expression heatmap of OsCPs in different tissues under normal conditions. (DOCX 2617Â kb)