Fig. 3: Evolutionary history of the oak genome.
a, Evolutionary scenario of oak from the AEK of 21 (post-γ) and 7 (pre-γ) protochromosomes reconstructed from a comparison of the Vitales (grape), Rosales (peach) and Malvales (cocoa) major subfamilies. The modern genomes (bottom) are illustrated with different colours reflecting the seven ancestral chromosomes of AEK origin (top). WGT (red star) refers to the whole-genome triplication (γ) shared among the eudicots. b, Ks distribution of gene pairs for oak–peach orthologues as well as the shared γ triplication in grape, peach, cocoa and oak. Ks distribution of all gene pairs in oak illuminate gene pairs from the γ triplication as well as recent duplicates. c, Dot plot representation of the oak genome against itself for the complete set of paralogous pairs (left) and without TDGs (right) representing the disappearance of the diagonal (TDGs) when low Ks values are removed. d, Expansion (524 orthogroups) and contraction (72 orthogroups) in oak relative to 15 other eudicot species. The pie charts reflect the contribution of TDGs, LDGs and singleton genes (SGs) to the significantly expanded and contracted orthogroups and to outstanding outliers (labelled 1–9). Numbers in square brackets associated with circle sizes stand for -log(P-value), computed from the oak branch-specific P-value provided by CAFE.
