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

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.