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…
Chloranthales, a lineage of angiosperms, is believed to have originated from an ancient allopolyploidization event involving ancestral monocot and eudicot lineages. This discovery was made through a comprehensive analysis of genomes from seven early-diverging angiosperm lineages, each having experienced only one lineage-specific whole-genome duplication (WGD) event.
The study utilized a phylogenomic framework to investigate the WGD-derived paralogs across five WGD-bearing lineages. Unlike other polyploid lineages, the WGD-derived paralogs in Chloranthales rarely formed sister relationships in gene trees. After considering various alternative explanations such as incomplete lineage sorting, ancient paralogy, and analytical artifacts, the researchers concluded that the discordant phylogenetic signal is indicative of the genomic legacy of an ancient allopolyploidization event.
By resolving the Chloranthales subgenomes using biased fractionation patterns within conserved syntenic regions, the study revealed that the dominant Chloranthales subgenome shares phylogenetic affinity with eudicots, while the recessive subgenome is associated with monocots. This finding suggests a deep reticulate origin involving ancestral lineages related to these major angiosperm clades.
The research provides subgenome-resolved evidence that ancient allopolyploidization played a crucial role in connecting deeply divergent lineages during early angiosperm evolution. The findings emphasize the importance of incorporating reticulate polyploid histories into phylogenomic frameworks for resolving deep evolutionary relationships.
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