Comparative genomics reveals the molecular basis of the synthesis of triterpenoid saponin and distinct flower morphology in Sapindaceae species

Sapindaceae, also named as soapberry family, is a large family of plants of great morphological diversities. The majority of them are monoecious, producing separate male and female flowers on the same plant. Some have petal-less flowers, some bear fruits with fleshy arils, and some are great source of certain secondary metabolites, like saponins. With the rapid development of next generation sequencing technologies, a number of Sapindaceae species have been sequenced, providing great resources for research from the perspective of comparative genomics analysis. Here, we sequenced and assembled a high-quality genome of balloon-vine (Cardiospermum halicacabum L.), the first liana plant with a full-genome sequenced in Sapindaceae, with the smallest genome size reported so far, low heterozygosity and repeatability, conferring it an ideal model plant for functional genomics research in Sapindaceae. In combination with other six publicly available Sapindaceae genomes, we reconstructed the Ancestral Sapindaceae karyotype (ASK) consisting of 18 protochromosomes and main chromosomal diversification fusion events shared or unique to these species. We characterized a Sapindale-specific biosynthetic gene cluster likely responsible for the biosynthesis of triterpenoid saponins in yellowhorn, soapberry and litchi. Intriguingly, we found that the absence of petals in litchi flowers is caused by the repressed expression of AP1 and AP3-1, two MADS-box genes essential for petal identity specification. Species-specific insertion of transposon elements in the promoter region of these two genes contributed to their expression repression via RNA-directed DNA methylation. Our work provides new insight and a great demonstration of using comparative genomics to dissect the molecular basis of characteristic trait development in Sapindaceae.无患子科（Sapindaceae）又名肥皂浆果科，是一类形态多样性极高的大型植物科。该科绝大多数物种为雌雄同株，可在同一植株上分别产生雄花与雌花。部分物种的花无花瓣，部分物种的果实带有肉质假种皮，还有部分物种是皂苷等次生代谢产物的优质来源。随着下一代测序技术的快速发展，已有多个无患子科物种完成全基因组测序，为比较基因组学研究提供了宝贵的数据资源。 本研究完成了倒地铃（Cardiospermum halicacabum L.）的全基因组测序与组装，该物种是无患子科中首个完成全基因组测序的藤本植物，其基因组大小为目前已报道的无患子科物种中最小，且杂合度与重复序列占比较低，是开展无患子科功能基因组学研究的理想模式植物。 结合另外6个已公开的无患子科物种基因组，本研究重构了包含18条原始染色体的无患子科祖先核型（Ancestral Sapindaceae Karyotype, ASK），并解析了这些物种共有的或物种特有的主要染色体进化融合事件。本研究还鉴定了一个无患子目特异性生物合成基因簇，该基因簇可能介导文冠果、肥皂浆果与荔枝中的三萜皂苷生物合成过程。 有趣的是，本研究发现荔枝花无花瓣的表型源于AP1与AP3-1两个基因的表达抑制：这两个MADS-box基因是调控花瓣身份特化的关键基因。这两个基因启动子区域的物种特异性转座子插入，通过RNA介导的DNA甲基化途径导致了其表达抑制。 本研究为利用比较基因组学解析无患子科物种特征性状发育的分子机制提供了全新视角与优质范例。