Comparative analysis of plastid genomes from allopolyploid Tragopogon miscellus and its diploid parents.

Tragopogon is a model system for the study of recent, recurrent, and reciprocal allopolyploid formation. Recent research has focused on the fates of nuclear genes duplicated in the allopolyploid T. miscellus relative to the parental diploids, T. dubius and T. pratensis. In contrast, little attention has been given to organellar genomes, which interact with the duplicated nuclear genomes via their gene products. Here we reconstructed plastid genomes (plastomes) for representatives of these three species to investigate their structure and variability among natural and synthetic allopolyploids. Genomic libraries were Illumina-sequenced for several individuals of the allopolyploid T. miscellus and its diploid parents. Whole plastomes were assembled from skimmed data with comparative analyses used to quantify structural and nucleotide variation. Tragopogon plastomes have a typical quadripartite structure and are similar in size to those of other Asteraceae. The 12 plastomes were highly similar, sharing ~99.5%-100% identity. In all but one case, the plastome sequence for each of the polyploids was most similar to that of its expected maternal parent. The exception involved a polyploid that unexpectedly had a T. dubius plastome type, likely as the result of backcrossing with its presumed paternal parent. Such backcrossing events may have contributed to the demise of this polyploid population. Plastome sequences can be used to infer the maternal origins of polyploids as well as investigate ongoing population-level dynamics. More fully assessing plastome variation across the geographic distribution of polyploids and their diploid progenitors may provide additional insights into polyploid formation, population dynamics, and subsequent evolution.