Orthologous synteny provides robust structural evidence for the ancestral angiosperm ε-WGD

The ancestral angiosperm whole-genome duplication (ε-WGD) is a pivotal yet contentious event that has long been debated. A recent study refuted its occurrence based on deviations from expected retention patterns of dosage-sensitive genes. Here, we provide both structural (orthologous synteny) and phylogenetic (subgenome-aware) evidence to revisit this debate. With improved annotation of the Ginkgo genome, we uncover a clear 1:2 orthologous synteny ratio between Ginkgo and early-diverging angiosperms ( Amborella and Aristolochia ), which lack lineage-specific WGDs. Subgenome-aware phylogenomic analyses further demonstrate that the Amborella / Aristolochia subgenomes diverged after the gymnosperm–angiosperm split but before the radiation of extant angiosperms. Together, these findings provide direct structural evidence for an ancestral angiosperm tetraploidization in the early Jurassic, following divergence from gymnosperms. We argue that the recent refutation of the ε-WGD relies on restrictive assumptions regarding ploidy level and duplicate retention that may not hold for deep-time polyploidy events. Our results provide a robust resolution to this long-standing debate and reaffirm the ε-WGD as a shared synapomorphy of extant angiosperms.