Phylotranscriptomics Reveal Multiple Whole-Genome Duplication Events and the Diversification History of Araceae

Polyploidy, or whole genome duplication (WGD) is widely regarded as key innovation promoting species diversification in plants. However, the hypothesis still remains controversial. Here, we tested the hypothesis by analyzing the association between polyploidy and the diversification of Araceae. Using 1081 single/low copy orthologous clusters from 90 transcriptome datasets, we generated a new time-calibrated phylogeny of Araceae. Based on Ks and gene tree methods, the special WGD event (abbreviation: ψ) was shared by the True Araceae clade, and not shared by Proto-Araceae and the lemnoids clade. By Analyses of time-dependent and trait-dependent diversification models, our results verified that the ψ WGD event was strongly associated with increases of net diversification rates of the True Araceae clade, but did not promote the diversification rates of Proto-Araceae and the lemnoids clade. Finally, functional enrichments analyses revealed that some genes in related to various binding, receptor and channel activity, DNA repair and cellular response to stress, such as heat shock protein, ABC transporter, Glycosyl hydrolase, RING finger, Pectin acetylesterase, Cytochrome P450 and Oxidative-stress-responsive kinase have experienced the expansions in the True Araceae clade. The expansions of these genes may contribute to the adaptation to the harsh tropical environment in the True Araceae clade. In summary, our results reconstructed the phylotranscriptomic framework of Araceae, revealed the diversification history of Araceae, and suggested that WGD may not act as the determining factor but the “Storage Cisterns” for species diversification.