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Data from: Revisiting ancient whole-genome duplications in the seed and flowering plants through the lens of dosage-sensitive genes

Shi, Tao1; Van de Peer, Yves2

Published Nov 21, 2025 on Dryad. https://doi.org/10.5061/dryad.gb5mkkx3z

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Nov 21, 2025 version files 25.80 MB

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Abstract

Whole-genome duplication (WGD) has been proposed as a catalyst for evolutionary innovation in seed plants and angiosperms, yet its occurrence remains contentious. By integrating gene dosage balance principles with phylogenomic reconciliation and probabilistic modeling, we revisit the debated ancestral seed and angiosperm WGDs. Leveraging dosage-sensitive orthologous gene groups (OGs) as evolutionary markers across representative plants for gene-tree/species-tree reconciliation, we demonstrate that gene retention patterns in Amborella and Aristolochia — early-diverging plants lacking post-angiosperm-origin WGDs — reveal a single gene duplication peak predating the seed plant diversification, with no signal of ancestral angiosperm WGD. Correlation analyses of observed and expected OG copy numbers given proposed WGD(s) further refute an angiosperm WGD. Probabilistic retention-modeling analysis corroborates these findings and shows that retention rates of dosage-sensitive genes from the putative angiosperm WGD are extremely low. Besides, our study establishes that genes inferred to have higher dosage sensitivity based on their sequential retention following WGD events may have increased utility in resolving ancestral polyploidy.