A super-pangenome framework of the genus Glycine unveils polyploid evolution and life-strategy transition

Abstract Polyploidy and life strategy transitions between annuality and perenniality often occur in flowering plants. However, the evolutionary propensities of polyploids and genetic bases of such transitions remain elusive. We assembled plantum genomes of representative perennial species across the genus Glycine including five diploids and a young allopolyploid, and constructed a Glycine super-pangenome framework by integrating 26 annual soybean genomes. The perennials exhibited greater genome stability than the annuals, with few centromere repeats abundant in the latter. Biased subgenome fractionation has occurred in the allopolyploid, primarily by accumulation of small deletions in gene clusters through illegitimate recombination, which was associated with preexisting local genomic differentiation. A gene annotated to modulate vegetative to reproductive phase transition was identified to have undergone adaptive evolution underlying the perenniality-annuality transition. Our study provides mechanistic insights into polyploid genome evolution and lays a foundation for unleashing genetic potential from the perennial gene pool for soybean improvement.