Evolutionary history and pan-genome dynamics of strawberry (Fragaria spp.)

Significance Strawberry is a very popular fruit. The strawberry genus (Fragaria) has emerged as a model system for various fundamental and applied research in recent years. Here, by using high-throughput sequencing technologies, we provide de novo whole-genome sequences for five wild strawberry species and genome resequencing data for 128 additional accessions of key species. Our analyses resulted in robust estimates of the evolutionary history for most diploid strawberry species, the discovery of a new diploid species (Fragaria emeiensis Jia J. Lei), and the construction of a pan-genome for strawberry. We also examined the evolutionary dynamics of gene families. This study provides a powerful genomic platform and resource for future studies in strawberry. Strawberry (Fragaria spp.) has emerged as a model system for various fundamental and applied research in recent years. In total, the genomes of five different species have been sequenced over the past 10 y. Here, we report chromosome-scale reference genomes for five strawberry species, including three newly sequenced species’ genomes, and genome resequencing data for 128 additional accessions to estimate the genetic diversity, structure, and demographic history of key Fragaria species. Our analyses obtained fully resolved and strongly supported phylogenies and divergence times for most diploid strawberry species. These analyses also uncovered a new diploid species (Fragaria emeiensis Jia J. Lei). Finally, we constructed a pan-genome for Fragaria and examined the evolutionary dynamics of gene families. Notably, we identified multiple independent single base mutations of the MYB10 gene associated with white pigmented fruit shared by different strawberry species. These reference genomes and datasets, combined with our phylogenetic estimates, should serve as a powerful comparative genomic platform and resource for future studies in strawberry.

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