Origin and evolution of the octoploid strawberry genome

TLDR

Cultivated strawberry originated from the hybridization of two wild octoploid species, each derived from four diploid progenitors that merged into a single nucleus over a million years ago. We present a near‑complete chromosome‑scale assembly of Fragaria × ananassa and investigate the origin and evolutionary processes shaping this complex allopolyploid. We identified extant relatives of each diploid progenitor, support a North American origin, revealed a single dominant subgenome with higher gene content, expression, and biased exchanges, and found that key metabolomic and disease‑resistance traits are largely governed by this subgenome, providing a platform for future evolutionary studies and molecular breeding.

Abstract

Cultivated strawberry emerged from the hybridization of two wild octoploid species, both descendants from the merger of four diploid progenitor species into a single nucleus more than 1 million years ago. Here we report a near-complete chromosome-scale assembly for cultivated octoploid strawberry (Fragaria × ananassa) and uncovered the origin and evolutionary processes that shaped this complex allopolyploid. We identified the extant relatives of each diploid progenitor species and provide support for the North American origin of octoploid strawberry. We examined the dynamics among the four subgenomes in octoploid strawberry and uncovered the presence of a single dominant subgenome with significantly greater gene content, gene expression abundance, and biased exchanges between homoeologous chromosomes, as compared with the other subgenomes. Pathway analysis showed that certain metabolomic and disease-resistance traits are largely controlled by the dominant subgenome. These findings and the reference genome should serve as a powerful platform for future evolutionary studies and enable molecular breeding in strawberry.