Tragopogon—a model for the study of recent and recurring polyploidy

Polyploidy is a common mechanism of speciation in plants and has been important in shaping the structure of plant genomes.  Within Compositae, polyploidy has played an especially important evolutionary role.  Analyses of polyploid evolution in the recently formed (early 1900s) allotetraploid species Tragopogon miscellus have yielded many new insights into genome evolution in polyploids.  Single-nucleotide polymorphisms (SNPs) identified through comparison of next-generation sequence data have been used in conjunction with Sequenom MassARRAY iPLEX genotyping to survey many loci in multiple individuals from several populations, with current analyses extending to hundreds of loci in hundreds of individuals.  We have found extensive evidence of homeolog loss in T. miscellus; these losses are not fixed in populations, but show repeatable patterns among populations of independent polyploid formation.  Moreover, patterns have emerged with regard to the physiological roles of genes retained in duplicate versus those returned to singleton status that are consistent with homeolog loss and retention of ancient gene duplications in Compositae.  Furthermore, some loci exhibit deviations from equal expression of parental homeologs, demonstrating that shifts in regulation can take place in a very short time.  Other loci show tissue-specific expression patterns, suggesting that subfunctionalization may also occur very quickly.  Using fluorescent and genomic in situ hybridization, we have characterized extensive chromosomal diversity in this young tetraploid species, perhaps providing mechanisms for the patterns of homeolog loss.  These analyses provide new perspectives on both the processes and consequences of polyploid speciation and on the role of genome duplication in plant evolution.