The Chrysanthemum nankingense genome provides insights into the evolution and diversification of chrysanthemum flowers and medicinal traits

Abstract The Asteraceae (Compositae), a large plant family of approximately 24 000–35 000 species, accounts for ∼10% of all angiosperm species and contributes a lot to plant diversity. The most representative members of the Asteraceae are the economically important chrysanthemums ( Chrysanthemum L.) that diversified through reticulate evolution. Biodiversity is typically created by multiple evolutionary mechanisms such as whole-genome duplication (WGD) or polyploidization and locally repetitive genome expansion. However, the lack of genomic data from chrysanthemum species has prevented an in-depth analysis of the evolutionary mechanisms involved in their diversification. Here, we used Oxford Nanopore long-read technology to sequence the diploid Chrysanthemum nankingense genome, which represents one of the progenitor genomes of domesticated chrysanthemums. Our analysis revealed that the evolution of the C . nankingense genome was driven by bursts of repetitive element expansion and WGD events including a recent WGD that distinguishes chrysanthemum from sunflower, which diverged from chrysanthemum approximately 38.8 million years ago. Variations of ornamental and medicinal traits in chrysanthemums are linked to the expansion of candidate gene families by duplication events including paralogous gene duplication. Collectively, our study of the assembled reference genome offers new knowledge and resources to dissect the history and pattern of evolution and diversification of chrysanthemum plants, and also to accelerate their breeding and improvement.