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.

近年来，草莓 ( Fragaria spp.) 已成为各种基础和应用研究的模型系统。在过去的 10 年中，总共对五种不同物种的基因组进行了测序。在这里，我们报告了五种草莓物种的染色体规模参考基因组，包括三个新测序物种的基因组，以及 128 个额外种质的基因组重测序数据，以估计关键草莓属物种的遗传多样性、结构和人口历史。我们的分析获得了大多数二倍体草莓物种的完全解析和强烈支持的系统发育和分化时间。这些分析还发现了一个新的二倍体物种（Fragaria emeiensis Jia J. Lei）。最后，我们为草莓构建了泛基因组并检查了基因家族的进化动态。值得注意的是，我们确定了与不同草莓物种共享的白色色素果实相关的MYB10基因的多个独立单碱基突变。这些参考基因组和数据集，与我们的系统发育估计相结合，应该成为草莓未来研究的强大比较基因组平台和资源。