Integrated metabolomics and transcriptomics analysis elucidate the candidate genes for polyphyllin biosynthesis in Paris

Polyphyllins are the key components in Paris, with varying levels and compositions among different species. This study investigated polyphyllin compositions of 206 Paris samples from 16 different producing areas. 9 Paris polyphylla var. yunnanensis, 3 Paris fargesii and 3 Paris forrestii were selected based on polyphyllin levels and composition for metabolome and transcriptome analysis. A total of 1243 metabolites and 1007 SCMs were identified among these samples, along with 92.11 Gb of full-length transcriptome data. Through a comprehensive analysis of the metabolome and transcriptome, a total of six 2,3-oxidized squalene cyclases (OSCs), 120 cytochrome P450s (CYPs) and 138 UDP-glycosyltransferases (UGTs) were annotated. Phylogenetic tree analysis narrowed down the candidate genes for OSC, CYP and UGT to 6, 12 and 26, respectively. By integrating metabolic and genetic differences, a total of 17 candidate genes including 2 OSCs, 4 CYPs and 11 UGTs, were identified. This study provides potential candidate genes involved in polyphyllins synthesis in Paris, aiming to facilitate the biosynthesis of different polyphyllins.