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.

菊科（菊科）是大约24000至35000种的大型植物科，约占所有被子植物种类的10％，对植物多样性做出了很大贡献。菊科中最具代表性的成员是具有经济意义的菊花（Chrysanthemum L.），它通过网状进化而多样化。生物多样性通常是通过多种进化机制创造的，例如全基因组复制（WGD）或多倍体化以及局部重复的基因组扩展。然而，由于缺乏来自菊花物种的基因组数据，无法深入分析其多样化所涉及的进化机制。在这里，我们使用牛津纳米孔长读技术对二倍体南宁菊花进行测序基因组，代表驯化菊花的祖细胞基因组之一。我们的分析表明C的演变。nankingense基因组是由重复元素扩增和WGD事件驱动的，其中包括最近的WGD区分了菊花和向日葵，向日葵从大约3880万年前与向日葵分离。菊花中观赏性和药用性状的变异通过复制事件（包括旁系同源基因复制）与候选基因家族的扩展有关。总的来说，我们对组装参考基因组的研究提供了新的知识和资源，以剖析菊花植物进化和多样化的历史和模式，并加速其育种和改良。