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The genes in polyphyllins pathway mixed with other steroid biosynthetic genes form an extremely complex biosynthetic network in  Paris polyphylla  with a giant genome. The lack of genomic data and tissue specificity causes the study of the biosynthetic pathway notably difficult. Here, we report an effective method for the prediction of key genes of polyphyllin biosynthesis. Full-length transcriptome from eight different organs via hybrid sequencing of next generation sequencingand third generation sequencing platforms annotated two 2,3-oxidosqualene cyclases (OSCs), 216 cytochrome P450s (CYPs), and 199 UDP glycosyltransferases (UGTs). Combining metabolic differences, gene-weighted co-expression network analysis, and phylogenetic trees, the candidate ranges of  OSC ,  CYP , and  UGT  genes were further narrowed down to 2, 15, and 24, respectively. Beside the three previously characterized CYPs, we identified the OSC involved in the synthesis of cycloartenol and the UGT (PpUGT73CR1) at the C-3 position of diosgenin and pennogenin in  P. polyphylla . This study provides an idea for the investigation of gene cluster deficiency biosynthesis pathways in medicinal plants.

Effective prediction of biosynthetic pathway genes involved in bioactive polyphyllins in Paris polyphylla