Breaking free: the genomics of allopolyploidy-facilitated niche expansion in white clover

The merging of distinct genomes, allopolyploidisation, generates adaptive potential through increased genetic diversity. Examples demonstrating exploitation of this potential are scarce, and the associated adaptive mechanisms remain unclear. White clover, Trifolium repens, is an allotetraploid forage crop derived from diploid T. occidentale and T. pallescens progenitors. Through genome and transcriptome sequencing of this species complex, we show the progenitor subgenomes have retained integrity and gene expression activity within white clover following allopolyploidisation ~45,000 years ago during the last glaciation. Born of climate change, white clover therefore represents a clear example of allopolyploidy-facilitated niche expansion, where the two progenitor genomes, originally adapted to disparate and highly specialised habitats, united and expanded to ubiquitous global presence following glaciation-induced allopolyploidisation. Underpinning this evolutionary success, we find high genetic diversity in white clover, indicating progenitor diversity carry-over through multiple hybridisation events, and we show that adaptive, tissue-specific expression switching occurs between homoeologous gene copies in a key flavonoid biosynthesis pathway.