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

First author: Chi Song; Affiliations: Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences (中国中医科学院中药研究所): Beijing, China

Corresponding author: Shilin Chen

The Asteraceae (Compositae 菊科), 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. 菊属) that were diversified by reticulate evolution (网状进化). Biodiversity is typically created by multiple evolutionary mechanisms such as whole-genome duplications (WGDs) or polyploidizations 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 (菊花脑) 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.

菊科植物大约含24000到35000个物种，具有非常高的植物多样性，占整个被子植物的10%左右。其典型代表属是具有较高经济价值菊属，该通过网状演化的方式进行物种间的分化。生物通过多种机制来增加物种的多样性，包括全基因组复制事件、多倍化事件及重复序列扩张等。然而，由于缺少菊属物种的参考基因组信息，对于菊属物种分化的研究受到严重的限制。本文作者通过Oxford纳米孔测序技术对二倍体的菊花脑进行了全基因组测序，菊花脑是现代驯化菊花的其中一个祖先物种。后续的分析显示菊花脑基因组的演化受到了重复序列爆发及近期基因组复制事件所驱动，该基因组复制事件将菊属物种与向日葵分化开来，时间大概在38.8个百万年左右。菊花脑园艺及药用性状方面的变异主要与由旁系同源基因复制所引起的一些候选基因的扩张相关。本文报道了第一份适用于研究菊属物种祖先基因集的参考基因组，这对于未来育种项目中研究菊花的遗传多样性具有非常重要的参考价值。

通讯：陈士林（http://www.icmm.ac.cn/Article/List_19.html#zgzkyry）

doi: https://doi.org/10.1016/j.molp.2018.10.003

Journal: Molecular Plant

Published date: 17 October, 2018

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