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

The Asteraceae (Compositae), a large plant family of approximately 24,000–35,000 species that strongly contributes to plant diversity, accounts for ∼10% of all angiosperm species. Its most representative members are the economically important chrysanthemums (Chrysanthemum L.) that were diversified by reticulate evolution. Biodiversity is typically created by multiple evolutionary mechanisms such as whole-genome duplications (WGDs) or polyploidisations and locally repetitive genome expansion. However, the lack of genomic chrysanthemum data prevents an in-depth analysis of the evolutionary mechanisms involved in chrysanthemum diversification. Here, we used the 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 elements and WGD events including a recent WGD that distinguishes chrysanthemum from the 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 that included paralogous gene duplication events. This is the first reference genome suitable for deriving the chrysanthemum progenitor gene set and critical for exploiting the genetic diversity of chrysanthemums in future breeding projects and beneficial applications.