Divergent genome fractionation and adaptation following polyploidy in the Araliaceae

Cyclic polyploidization/diploidization is a driving force in the evolution of eukaryotes. It remains unclear how post-polyploidy reshuffling of ancestral genomes is correlated with evolutionary and ecological diversification. The Araliaceae consists of > 1500 diverse species of herbs, shrubs and trees, which have undergone several polyploidization/diploidization events and have adapted to different forest ecosystem habitats. Here, by leveraging 20 genomes/subgenomes and 561 transcriptomes, we demonstrate that the genome architecture and transcriptional landscape of extant Araliaceae have undergone remodeling associated with polyploidizations/diploidizations. Phenotypic comparisons revealed that phylogenetically distinct species of the Araliaceae have repeatedly evolved shade- and open-habitat phenotypes, accompanied by leaf morphology, efficiency of photosynthesis and carbon fixation. Biased genetic fractionation and transcriptional remodeling of the photomorphogenesis (e.g. PhyB and PIFs) and photosynthesis (e.g. Lhcb-1 and Rubisco) networks are associated with this ecological adaptation. Our study provides evidence that post-polyploidy reshuffling and fractionation correlate with phenotypic and ecological diversification.