Ancient allopolyploidy and specific subgenomic evolution drove the radiation of poplars and willows.

Allopolyploidy involves the fusion of genomes from different lineages through hybridization and chromosome doubling. However, detecting early allopolyploidy events and understanding the specific subgenomic evolution that contributes to the origin of adaptive innovations for species radiation can be challenging. Here, we present genomes representing all three subfamilies of Salicaceae, a woody model clade, and collect epigenetic and transcriptomic samples. We reveal one shared ancient allopolyploidy event involving Populus, Salix and two sister genera, followed by contrasted karyotypic and subgenomic evolution. The specific evolution sets the stage for the origin of novel photoperiod responses, flowering phenology and small-hairy seeds in the highly speciose Populus and Salix compared with their species-depauperate sister genera, which may lead to their ecological adaptation and radiation. Our findings underscore the role of ancient allopolyploidization and specific subgenomic evolution in driving both innovation and species diversification at deep nodes of the plant tree of life.