The garden strawberry (Fragaria × ananassa) is an octoploid — it carries eight copies of each chromosome instead of the usual two — and biologists have long struggled to explain exactly how that came to be. A study published in Horticulture Research in 2025 now offers the clearest evolutionary account yet: the cultivated strawberry’s genome was assembled not in one event but across three separate hybridization episodes, stitched together from at least four different ancestral genomes, some of which no longer exist in a form scientists can directly sample.
Why the strawberry genome is so hard to read
Octoploid genomes are notoriously difficult to untangle. When a species’ genome is duplicated across four ancestral lineages, as in cultivated strawberry, every chromosome has three “sibling” copies inherited from different progenitors, and standard comparative-genomics tools struggle to tell them apart, especially when one or more of the original parent species is missing from modern collections or extinct outright.
The research team — led by Qingyi Yu and Haomin Lyu of the USDA Agricultural Research Service’s Tropical Plant Genetic Resources and Disease Research Unit at the Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center in Hilo, Hawaii, together with Shujun Ou of Ohio State University’s Department of Molecular Genetics and Won Cheol Yim of the University of Nevada’s Department of Biochemistry and Molecular Biology — built a new computational method specifically to get around that problem.
Reading transposable elements as evolutionary clocks
Rather than relying on a known set of diploid ancestors as a reference (the conventional approach, and one that fails when an ancestor is missing or extinct), the team developed what they call a serial similarity matrix (SSM) method built on long terminal repeat retrotransposons (LTR-RTs) — a class of transposable element that inserts new copies of itself throughout a genome over time and then slowly accumulates mutations at a roughly predictable rate.
Because that decay is measurable, LTR-RTs function as molecular timestamps: comparing how much a genome’s LTR-RT insertions have diverged from one another lets researchers estimate when a subgenome split off, without needing a living relative to compare it against directly. Applying that method to the cultivated strawberry genome, the researchers say, allowed them to reconstruct polyploid history “without relying on known ancestor species” — a specific limitation of prior approaches that this method was designed to solve.
Three hybridization events, four subgenomes
The analysis identified four distinct subgenomes within the cultivated strawberry and traced their assembly to three sequential allopolyploidization events — hybridizations between different species that also duplicated the resulting chromosome set, rather than simple duplications within one lineage. The team’s dating placed these three events at roughly 3.1–4.2 million years ago, 1.9–3.1 million years ago, and 0.8–1.9 million years ago, with the subgenomes showing their closest surviving relationships to two wild diploid species, Fragaria vesca (the woodland strawberry) and Fragaria iinumae.
That staged picture matters because it means the modern dessert strawberry is not the product of a single ancient hybridization but a compound one — several distinct wild lineages contributing genetic material at different points, some of which may no longer be represented by any species available for direct sequencing today.
Why this matters beyond strawberry breeding
Cultivated strawberry is one of many economically important crops — alongside wheat, cotton, and canola — that are polyploid, and untangling which ancestral genome contributed which traits is a prerequisite for precision breeding: knowing which subgenome carries a disease-resistance gene, for instance, makes it possible to select for or introgress that trait more precisely. Because the SSM method doesn’t require a complete set of known living ancestors, it is also a tool other polyploid-genome research groups can apply to species where the full ancestral lineage isn’t available for comparison — a common problem across polyploid crop genomics generally, not one unique to strawberry.
The study’s data availability statement notes that the analysis code underlying the SSM method is openly published on GitHub, letting other genome-assembly groups apply the same subgenome-partitioning approach to their own polyploid datasets without re-deriving the method from scratch — a routine but consequential piece of open-science practice in comparative genomics, where reproducible, re-usable analysis pipelines are increasingly expected alongside the sequence data itself.
Source
Lyu, H., Ou, S., Yim, W.C., & Yu, Q. (2025). “Deciphering octoploid strawberry evolution with serial LTR similarity matrices for subgenome partition.” Horticulture Research, 12(8). DOI: 10.1093/hr/uhaf132. Summarized by ScienceDaily (June 19, 2026), based on materials from the American Society for Horticultural Science.
