<i>PtaJAZ3</i>- and <i>PtaRAP2</i>.<i>6-</i>centered networks.

Both the regulatory networks were generated using Algorithm for the Reconstruction of Accurate Cellular Networks (ARACNE) analysis (see experimental procedures). The two superhubs (squares) were connected to four hub genes (hexagons) which in turn were connected to terminal genes (circles). Abbreviations for the four hubs connected to PtaJAZ3 are as follows: 1. PtaCYCB2;4 (Cycline B2;4, Potri.005G251400); 2. PtaSAUR37 (Small Auxin Upregulated RNA 37, Potri.006G278100); 3.PtaARFA1F (ADP-Ribosylation Factor A1F, Potri.008G100000); 4. PtaGH16 (Glycosyl Hydrolases family 16, Potri.006G071200). Abbreviations for the four hubs connected to PtaRAP2.6 are as follows: 1. PtaGRF (Gibberellin-Regulated Family protein, Potri.014G020100); 2. PtaEBF1 (EIN3-Binding F-box protein1, Potri.006G068500); 3. PtaCDC2 (Cell Division Control 2, Potri.004G133500); 4. PtaXTH23 (Xyloglucan Endotransglucosylase/Hydrolase 23, Potri.018G095100). Details of the terminal genes connected to individual hubs are provided in S4 Data and S1 Table.