A Combination of Genetic Mapping and Phylogenetics Untangles the Cryptic Hybrid Origin of a Decaploid Strawberry

Polyploidy plays an essential role in promoting plant diversification and domestication. While the widespread incidence of polyploidy in monocots and eudicots is well documented, the origins of most extant polyploid species remain largely unknown, especially those of high-order polyploids that potentially underwent complex processes of genome merging and doubling over variable timeframes. Here we investigated the evolutionary origin of a recently discovered decaploid strawberry (Fragaria cascadensis), which was hypothesized to have originated from contemporary sympatric speciation between the diploid F. vesca subsp. bracteata (of Av genome) and octoploid F. virginiana subsp. platypetala (of subgenomes Av, Bi, B1 and B2) in North America. Using an integrated approach of genetic mapping and phylogenetics, we found that the decaploid strawberry genome consists of the octoploid subgenomes (Av, Bi, B1 and B2) and an extra copy of subgenome B1 or B2 derived from an extinct close relative of F. iinumae. In marked contrast to the leading hypothesis on the basis of present-day sympatry, our findings support a scenario of old polyploid hybrid speciation between the octoploid and an extinct F. iinumae-like diploid, which was also a progenitor contributing to the octoploid clade formation during the Pleistocene likely in Beringia.