Comparative proteomics of the recently and recurrently formed natural allopolyploid Tragopogon mirus (Asteraceae) and its parents

We examined the proteomes of the recently formed natural allopolyploid Tragopogon mirus and its diploid parents (T.similar to dubius, T.similar to porrifolius), as well as a diploid F1 hybrid and synthetic T.similar to mirus. Analyses using iTRAQ LC-MS/MS technology identified 476 proteins produced by all three species. Of these, 408 proteins showed quantitative additivity of the two parental profiles in T.similar to mirus (both natural and synthetic); 68 proteins were quantitatively differentially expressed. Comparison of F1 hybrid, and synthetic and natural polyploid T.similar to mirus with the parental diploid species revealed 32 protein expression changes associated with hybridization, 22 with genome doubling and 14 that had occurred since the origin of T.similar to mirus c. 80 yr ago. We found six proteins with novel expression; this phenomenon appears to start in the F1 hybrid and results from post-translational modifications. Our results indicate that the impact of hybridization on the proteome is more important than is polyploidization. Furthermore, two cases of homeolog-specific expression in T.similar to mirus suggest that silencing in T.similar to mirus was not associated with hybridization itself, but occurred subsequent to both hybridization and polyploidization. This study has shown the utility of proteomics in the analysis of the evolutionary consequences of polyploidy.