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