title: Comparative proteomics of the recently and recurrently formed natural allopolyploid Tragopogon mirus (Asteraceae) and its parents.
abstract: • We examined the proteomes of the recently formed natural allopolyploid Tragopogon mirus and its diploid parents (T. dubius, T. porrifolius), as well as a diploid F(1) hybrid and synthetic T. 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. mirus (both natural and synthetic); 68 proteins were quantitatively differentially expressed. • Comparison of F(1) hybrid, and synthetic and natural polyploid T. 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. mirus c. 80 yr ago. We found six proteins with novel expression; this phenomenon appears to start in the F(1) 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. mirus suggest that silencing in T. 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.
authors.affiliation: Department of Biology, University of Florida, Gainesville, FL 32611, USA.|Interdisciplinary Center for Biotechnology Research, University of Florida, PO Box 103622, Gainesville, FL 32610, USA.
authors.forename: Jin
authors.initials: J
authors.lastname: Koh
authors.affiliation: Department of Biology, University of Florida, Gainesville, FL 32611, USA.|Interdisciplinary Center for Biotechnology Research, University of Florida, PO Box 103622, Gainesville, FL 32610, USA.|Genetics Institute, University of Florida, Gainesville, FL 32610, USA.
authors.forename: Sixue
authors.initials: S
authors.lastname: Chen
authors.affiliation: Department of Biology, University of Florida, Gainesville, FL 32611, USA.
authors.forename: Ning
authors.initials: N
authors.lastname: Zhu
authors.affiliation: Interdisciplinary Center for Biotechnology Research, University of Florida, PO Box 103622, Gainesville, FL 32610, USA.
authors.forename: Fahong
authors.initials: F
authors.lastname: Yu
authors.affiliation: Genetics Institute, University of Florida, Gainesville, FL 32610, USA.|Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA.
authors.forename: Pamela S
authors.initials: PS
authors.lastname: Soltis
authors.affiliation: Department of Biology, University of Florida, Gainesville, FL 32611, USA.|Genetics Institute, University of Florida, Gainesville, FL 32610, USA.
authors.forename: Douglas E
authors.initials: DE
authors.lastname: Soltis
mesh_terms: D000595:Amino Acid Sequence; D002452:Cell Count; D048429:Cell Size; D003433:Crosses, Genetic; D004171:Diploidy; D018506:Gene Expression Regulation, Plant; D007553:Isotope Labeling; D018515:Plant Leaves / Q000378:metabolism; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D011123:Polyploidy; D020543:Proteome / Q000378:metabolism; D040901:Proteomics / Q000379:methods*; D011523:Protoplasts / Q000166:cytology / Q000378:metabolism; D017386:Sequence Homology, Amino Acid; D013045:Species Specificity; D031188:Tragopogon / Q000166:cytology / Q000235:genetics* / Q000378:metabolism*; D014158:Transcription, Genetic
chemical_list: D010940:Plant Proteins; D020543:Proteome