Discovering subgenomes of octoploid strawberry with repetitive sequences

Although its sequence was recently determined in a genomic tour de force ,{[Edger 2019][1]} the ancestry of the cultivated octoploid strawberry Fragaria x ananassa remains controversial.{[Liston 2020][2]; [Edger 2020][3]} Polyploids that arise by hybridization generally have chromosome sets, or subgenomes, of distinct ancestry.{Stebbins 1947; Garsmeur 2014} The conventional method for partitioning a polyploid genome into its constituent subgenomes relies on establishing phylogenetic relationships between protein-coding genes of the polyploid and its extant diploid relatives,{Edger 2018-sub} but this approach has not led to a consensus for cultivated strawberry.{[Liston 2020][2]; [Edger 2020][3]} Here we resolve this controversy using a complementary strategy that focuses on the chromosomal distribution of transposable elements and depends only on the octoploid sequence itself.{[Session 2016][4]; [Mitros 2020][5]} Our method independently confirms the consensus that two of the four subgenomes derived from the diploid lineages of F. vesca and F. iinumae .{[Tennessen 2014][6]; [Edger 2019][1]} For the remaining two subgenomes, however, we find a statistically well-supported partitioning that differs from ref. {[Edger 2019][1]} and other work (reviewed in {[Hardigan 2020][7]}). We also provide evidence for a shared allohexaploid intermediate and suggest a neutral explanation for the “dominance” of the F. vesca -related subgenome. ### Competing Interest Statement The authors have declared no competing interest. [1]: #ref-1 [2]: #ref-2 [3]: #ref-3 [4]: #ref-5 [5]: #ref-6 [6]: #ref-7 [7]: #ref-9