1. 1 Supplemental Figure 1 Expression analysis of MPF1-like Withania duplicates The RNAs isolated from leaves, flower buds, sepals, stamens, carpels and siliques of Withania somnifera were subjected to real time RT-PCR analysis with gene-specific primers. The columns show the expression of MPF1-like-A of Withania (WSA106; white) and MPF2-like-B of Withania (WSB106; grey)). The values given are relative expression based on three independent experiments normalized with respect to 18S rRNA. Error bars indicate the standard deviation.

2. 2 Supplemental Figure 2 -2.2kb -1.7kb -1.1kb-1bp-559 bp Supplemental Figure 2 Mulan (Multiple-sequence local alignment; http://mulan.dcode.org) image of individual MPF2 promoter sequencehttp://mulan.dcode.org Putative cis-acting elements in the promoters were predicted using the plant cis-acting regulatory DNA elements database Transfac (http://www.gene-regulation.com/pub/databases.html). Concatenated tba.maf files were submitted to MultiTIF in TRANSFAC professional V10 library from plants and matrix similarity optimized for functions was predefined as 0.85. Eleven out of 80 plant transcription factor families were selected for the creation of TBX5 and NKX 2.5 high quality matrix. The parameters selected for the dynamic overlay of transcription factor binding sites (TFBS) prediction with conservation profile clustering included: 3 kb per layer, picture width of 1200 pixels, one site per 1000 bp and clustering with smooth plot. Finally, the dynamic visualization of TFBS was attained in a graphical format. Scale is also indicated at the base (http://mulan.dcode.org).http://www.gene-regulation.com/pub/databases.htmlhttp://mulan.dcode.org

3. 3 Supplemental Figure 3 Graphical output shows MPF2-like %age GC contents in a sliding window of 20bp in a range of 0 to 100% Multiple sequence alignment of -2kb promoter region of Solanum, Withania, Tubocapsicum, Physalis and Vassobia was performed with ClustalW program in MacVector software. Shaded area indicates the highest GC content region. Cis-regulatory modules (CRM1, CRM2 and CRM3) are shown on the top of shaded region. A rough scale is also indicated.