RNA-seq analysis of Paris polyphylla var. yunnanensis roots identified candidate genes for saponin synthesis

Paris polyphylla Smith var. yunnanensis (Franch.) Hand.-Mazz. is a rhizomatous, herbaceous, perennial plant that has been used for more than a thousand years in traditional Chinese medicine. It is facing extinction due to overharvesting. Steroids are the major therapeutic components in Paris roots, the commercial value of which increases with age. To date, no genomic data on the species have been available. In this study, transcriptome analysis of an 8-year-old root and a 4-year-old root provided insight into the metabolic pathways that generate the steroids. Using Illumina sequencing technology, we generated a high-quality sequence and demonstrated de novo assembly and annotation of genes in the absence of prior genome information. Approximately 87,577 unique sequences, with an average length of 614 bases, were obtained from the root cells. Using bioinformatics methods, we annotated approximately 65.51% of the unique sequences by conducting a similarity search with known genes in the National Center for Biotechnology Information's non-redundant database. The unique transcripts were functionally classified using the Gene Ontology hierarchy and the Kyoto Encyclopedia of Genes and Genomes database. Of 3082 genes that were identified as significantly differentially expressed between roots of different ages, 1518 (49.25%) were upregulated and 1564 (50.75%) were downregulated in the older root. Metabolic pathway analysis predicted that 25 unigenes were responsible for the biosynthesis of the saponins steroids. These data represent a valuable resource for future genomic studies on this endangered species and will be valuable for efforts to genetically engineer P. polyphylla and facilitate saponin-rich plant development.