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Abstract
Ancient whole-genome duplications (WGDs or polyploidy) are prevalent in plants, and
some WGDs occurred during the timing of severe global environmental changes. It has
been suggested that WGDs may have contributed to plant adaptation. However, this still
lacks empirical evidence at the genetic level to support the hypothesis. Here, we
investigated the survivors of gene duplicates from multiple ancient WGD events on
the major branches of angiosperm phylogeny, and aimed to explore genetic evidence
supporting the significance of polyploidy. Duplicated genes co-retained from three
waves of independent WGDs (∼120 million years ago [Ma], ∼66, and <20 Ma) were investigated
in 25 selected species. Gene families functioning in low temperature and darkness
were commonly retained gene duplicates after the eight independently occurring WGDs
in many lineages around the Cretaceous-Paleocene boundary, when the global cooling
and darkness were the two main stresses. Moreover, the commonly retained duplicates
could be key factors which may have contributed to the robustness of the critical
stress-related pathways. In addition, genome-wide transcription factors (TFs) functioning
in stresses tend to retain duplicates after waves of WGDs, and the coselected gene
duplicates in many lineages may play critical roles during severe environmental stresses.
Collectively, these results shed new light on the significant contribution of paleopolyploidy
to plant adaptation during global environmental changes in the evolutionary history
of angiosperms.