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.

古代的全基因组重复（WGD或多倍体）在植物中很普遍，一些WGD在严重的全球环境变化时期发生。有人建议，WGDs可能有助于植物适应。但是，这在遗传水平上仍然缺乏支持该假说的经验证据。在这里，我们调查了被子植物系统发育主要分支上多个古代WGD事件的基因重复序列的幸存者，旨在探索支持多倍体意义的遗传证据。在25个选定的物种中研究了三波独立WGD（〜1.2亿年前[Ma]，〜66和<20 Ma）共保留的重复基因。在低温和黑暗中起作用的基因家族通常是保留在白垩纪-古新世边界周围许多世系中的八个独立发生的WGD之后的基因重复片段，而全局冷却和黑暗是两个主要压力。此外，通常保留的重复项可能是关键因素，可能有助于关键压力相关途径的鲁棒性。此外，在应激中起作用的全基因组转录因子（TFs）倾向于在WGD波动后保留重复序列，并且许多谱系中的共同选择的基因重复序列可能在严重的环境应激中起关键作用。总的来说，这些结果为在被子植物进化史中全球环境变化过程中古多倍体对植物适应性的重大贡献提供了新的启示。