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bioRxiv · 10.1101/2020.11.04.330431

Discovering subgenomes of octoploid strawberry with repetitive sequences

Session, A. M.·Rokhsar, D. S.
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Abstract

Although its sequence was recently determined in a genomic tour de force,{Edger 2019} the ancestry of the cultivated octoploid strawberry Fragaria x ananassa remains controversial.{Liston 2020; Edger 2020} 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; Edger 2020} 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; Mitros 2020} 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; Edger 2019} For the remaining two subgenomes, however, we find a statistically well-supported partitioning that differs from ref. {Edger 2019} and other work (reviewed in {Hardigan 2020}). We also provide evidence for a shared allohexaploid intermediate and suggest a neutral explanation for the "dominance" of the F. vesca-related subgenome.

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Session, A. M., Rokhsar, D. S.. 2020-11-05. Discovering subgenomes of octoploid strawberry with repetitive sequences. https://doi.org/10.1101/2020.11.04.330431

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