Fig. 4

Phylogenetic inference of the timing of duplication for differentially expressed guayule transcripts. (a) Chronogram of the four species used to build gene trees for this analysis. Placement of markers representing whole genome triplication (hexagons) and duplication (squares) indicates whether an event occurred in a common ancestor and is therefore shared (e.g. purple hexagon indicates a genome triplication event in the last common ancestor to all Asteraceae), or if it is species-specific (e.g., the light blue square for guayule represents the duplication event in the accession examined in this study, AZ-3). (b) The two phylogenetic models used to infer timing of the duplicated transcripts observed in guayule. Left, duplicated guayule transcripts, represented by P. arg-A and -B are sister to H. annuus paralogs, represented by H. ann-A and H. ann-B and thus likely originated from the whole genome triplication event at the base of the Asteraceae (purple hexagon). Right, guayule paralogs are sister to one another in the gene tree and then to a H. annuus ortholog, suggesting a guayule specific duplication event (light blue square). (c) Bar plot indicating the number of differentially expressed guayule transcripts associated with each duplication event. Duplication events inferred to have arisen specifically in guayule (AZ-3) are shown in light blue, whereas those likely originating from the ancient Asteraceae hexaploidy event are shown in purple, using the same color scheme from a and b. Pseudogenization of one of the guayule paralogs is indicated by the tan bar. (d) Gene tree representing an AZ-3 specific duplication event (blue box). (e) Gene tree representing an Asteraceae event (purple box). In d and e, gene trees were rooted using the Arabidopsis ortholog