Multiple Fragaria species sequenced to evaluate octoploid progenitors Phenotype or Genotype

Whole-genome duplications are radical evolutionary events that drive speciation and adaptation in many taxa. The hybrid origins and dynamic restructuring of polyploid genomes are poorly understood due to the challenge of distinguishing homeologous sequences. We use dense targeted-capture-based linkage maps to improve the diploid strawberry (Fragaria vesca) reference genome and to disentangle the octoploid subgenomes of F. virginiana and F. chiloensis. Our novel approach, POLiMAPS, associates informative inter-homeolog phylogenetic markers with linkage groups and reference genome positions. Upending a widely accepted model, we find that three subgenomes originate with F. iinumae and only one with F. vesca. Extensive unidirectional gene conversion has made the F. iinumae-like subgenomes more F. vesca-like and divergent from each other, likely for adaptive reasons. Divergence among homeologs is also facilitated by interchromosome transpositions. We reveal the complex genomic exchanges underlying polyploid evolution and present a path to unravel other polyploid genomes of agricultural and evolutionary importance.