Abstract
The Araliaceae family has significant economic and medicinal value. However, the phylogenetic relationships and the expression patterns of key genes of the active triterpenoid substance within this family are still unclear. In this study, we employed comparative transcriptomics to analyze the transcriptomes of 19 species from 11 genera of Araliaceae, aiming to elucidate the evolutionary history of the family and the expression patterns of key genes in the ginsenoside biosynthesis pathway. Our results divide Araliaceae into two subfamilies: Aralioideae and Hydrocotyloideae. Aralioideae is further classified into three groups: the Aralia-Panax group, the Polyscias-Pseudopanax group, and the Asian Palmate group. PhyloNet analysis reveals that the common ancestor of Panax ginseng, Panax quinquefolius, and Panax japonicus was an allopolyploid, likely resulting from hybridization between Panax notoginseng and Panax pseudoginseng. Additionally, all Aralioideae species underwent the pg-β event, which may be critical for ginsenoside biosynthesis. We discovered that Panax species exhibit distinct expression patterns of key enzyme genes (β-AS, DDS, CYP450, UGTs) compared to other Araliaceae species. These enzyme genes show independent evolutionary lineages in gene trees, suggesting unique functional adaptations that enable Panax species to efficiently synthesize ginsenosides. This study provides a theoretical foundation for the conservation and utilization of Araliaceae germplasm resources.