Ancient allopolyploidy and specific subgenomic evolution drive adaptive radiation in poplars and willows

Allopolyploidy involves the fusion of genomes from different lineages through hybridization and chromosome doubling. However, detecting early allopolyploidy events in evolutionary history and understanding the specific subgenomic evolution that contributes to the origin of adaptive innovations for species radiation can be challenging. Here, we sequenced the genomes representing all three subfamilies of Salicaceae, a woody model clade, and collected epigenetic and transcriptomic samples. We revealed one shared ancient allopolyploidy event involving Populus, S alix and two sister genera, but followed by contrasted karyotypic and subgenomic evolution. The specific evolution drove the origin of unique photoperiod adaptation, flowering phenology and small, hairy seeds in the highly speciose Populus and Salix when compared with their species-depauperate sister genera. These adaptive traits may have ultimately led to the ecological adaptations and species radiation in both poplars and willows. Our findings underscore the previously overlooked role of ancient allopolyploidization and specific subgenomic evolution for fostering adaptive innovation and species diversification at deep nodes of the plant tree of life. One sentence summary: The specific subgenome evolution after ancient allopolyploidy drives the origin of unique adaptive traits that promote species radiation of the highly speciose Populus (poplars) and Salix (willows).