Subgenome-Level Phylogeny Reveals an Allopolyploid Origin of Chloranthales from Ancestral Monocot and Eudicot Lineages

Angiosperms (flowering plants) represent the most species-rich lineage of land plants, yet deep phylogenetic relationships among their major clades, particularly within mesangiosperms, remain notoriously difficult to resolve. Although hybridization and whole-genome duplication (WGD) are recognized as major evolutionary forces, the contribution of ancient allopolyploidization, which combines hybridization with WGD, to deep-node phylogenetic discordance in mesangiosperms remains poorly understood. Here, we analyzed genomes from seven representative early-diverging angiosperm lineages, each containing no more than one lineage-specific WGD event. Using a comparative phylogenomic framework, we characterized WGD-derived paralogs across five WGD-bearing lineages. In contrast to other polyploid lineages, Chloranthales WGD-derived paralogs rarely formed sister relationships in gene trees. After evaluating alternative explanations, including incomplete lineage sorting, ancient paralogy, and analytical artifacts, we demonstrate that this discordant phylogenetic signal reflects the genomic legacy of an ancient allopolyploidization event. We further resolved the Chloranthales subgenomes by exploiting biased fractionation patterns within conserved syntenic regions. Subgenome-resolved phylogenomic analyses revealed that the dominant Chloranthales subgenome exhibits phylogenetic affinity with eudicots, whereas the recessive subgenome is associated with monocots, indicating a deep reticulate origin involving ancestral lineages related to these major angiosperm clades. Our findings provide subgenome-resolved evidence that ancient allopolyploidization can connect deeply diverged lineages during early angiosperm evolution, highlighting the importance of incorporating reticulate polyploid histories into phylogenomic frameworks for resolving deep evolutionary relationships.