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.