The origin and subgenome dynamics of the octoploid strawberries

The octoploid strawberries include the cultivated Fragaria ×ananassa and its two wild progenitors, F. chiloensis and F. virginiana. These two progenitors share a common origin an estimated one million years ago. The 2019 publication of the F. ×ananassa 'Camarosa' genome sequence has provided new opportunities to identify the diploid ancestry of the four subgenomes comprising the octoploid genome. Studies agree that two of the diploid ancestors are western North American F. vesca subsp. bracteata and East Asian F. iinumae. The identity of the other two subgenomes is controversial. One hypothesis presented in the genome publication implicates the extant diploids F. nipponica from Japan and F. viridis from western Eurasia. The second hypothesizes that these two subgenomes originated from an extinct species most closely related to F. iinumae and may represent an ancestral autotetraploid. A new phylogenomic analysis using a 10-fold increase in the number of data points strongly supports the second hypothesis. This high-resolution analysis finds that chromosomal segments from the vesca subgenome have replaced approximately 5% of the other 3 subgenomes. This process of homeologous exchange (HE) has occurred in regions of significantly higher gene content, suggesting an adaptive basis. These regions are expected to have less orthologous gene diversity due to this sequence replacement. Putative HE to the vesca subgenome is less frequent (3.9%) and occurs in smaller segments in significantly gene poor regions, indicating that it may be the result of non-adaptive processes. A small fraction (0.23%) of the vesca subgenome shows evidence of potential reciprocal HE with one or more of the other three subgenomes. Identifying the diploid progenitors of the octoploid will illuminate the environment and potential selective forces experienced by each subgenome prior to their merger into a single genome. This legacy has shaped the genetic variation available for breeding and crop improvement in strawberry. For this reason, it is critically important to correctly reconstruct these evolutionary events.