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Fig. S1 Example of cation exchange chromatography of iTRAQ labeled peptides derived from Tragopogon porrifolius, T. dubius, T. mirus, the diploid hybrid, and the synthetic allopolyploid.

Fig. S2 Novel expression in diploid F1 hybrids and protein posttranslational modifications (PTMs).

Table S1 Primer sequences using quantitative Real-time RT-PCR

Table S2 Number of proteins identified at critical false discovery rates from three analyses

Table S3 476 identified proteins from all three species

Table S4 Expression patterns in Tragopogon mirus inferred from quantitative Real-time PCR

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