Phylogenomics of Glycine unveils evolutionary propensities of polyploidy and perenniality. Phylogenomics of Glycine unveils evolutionary propensities of polyploidy and perenniality

Polyploidy and evolutionary transitions between annuality and perenniality often occur in flowering plants; however, the evolutionary propensities and/or genetic bases of such events, and their impacts on genomic diversification, adaptation, and speciation remain elusive. Here we report construction of a platinum panortholome of perennial soybean species across the Glycine genus including five diploids (paleopolyploids) and a young allopolyploid native to Australia, and phylogenomic analyses that include annual soybeans native to Eastern Asia. Despite a high degree of genomic collinearity among the diploids, there are species-specific chromosomal rearrangements and emergence/turnover of genes and transposons. Compared with the annuals, the perennials exhibited lower frequencies of genomic rearrangements and lower evolutionary rates, but nearly complete absence of centromere repeats found in the annuals. Despite few transposon insertions and genomic rearrangement events after the formation of the young allopolyploid, biased subgenome fractionation has occurred, primarily by accumulation of small deletions in gene clusters through illegitimate recombination, which was associated with preexisting differentiation of evolutionary rates and expression levels of genes between the ancestral diploids. Candidate genes underlying perenniality were identified. This study provides mechanistic insights into polyploid and perennial genome evolution and marks a milestone in unleashing genetic potential from this intercontinental gene pool for soybean improvement