Genome sequences (.fa), amino acid sequences (.pep), coding sequences (.cds), and genome annotation files (.gff3) of Fragaria chinensis (Fch), F. corymbosa (Fco), F. moupinensis (Fmo), F. pentaphylla (Fpe), and F. daltoniana (Fda).

Over the decades, evolutionists and ecologists have shown intense interest in the role of polyploidization in plant evolution. Without clear knowledge of the diploid ancestor(s) of polyploids, we would not be able to answer fundamental ecological questions such as the evolution of niche differences between them or its underlying genetic basis. Here, we explored the evolutionary history of two Fragaria tetraploids, F. corymbosa and F. moupinensis. We de novo assembled five genomes including these two tetraploids and three diploid relatives (F. chinensis, F. pentaphylla and F. daltoniana). Based on multiple lines of evidence, we found no evidence of distinct subgenomes in either of the two tetraploids, suggesting autopolyploid origins. Using phylogenomic approaches, we determined that F. chinensis was the closest diploid relative of both F. corymbosa and F. moupinensis. Genome resequencing data suggested signals of introgression between F. chinensis and F. pentaphylla, leading to the observed genomic similarity between these two diploids. Compared to F. chinensis, gene families related to high ultraviolet (UV)-B and DNA repair were expanded, while those that responded towards abiotic and biotic stresses (such as salt stress, wounding, and various pathogens) were contracted in both tetraploids. Furthermore, transcriptomic data indicated that the tetraploids tended to down-regulate defense response genes but up-regulate UV-B response, DNA repairing, and cell division gene expression compared to F. chinensis. These findings may reflect adaptions toward high-altitude habitats. In summary, our work provides insights into the genome evolution of wild Fragaria tetraploids and opens up an avenue for future works to answer deeper evolutionary and ecological questions regarding the strawberry genus.