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Background The investigation of molecular mechanisms involved in polysaccharides and saponin metabolism is critical for genetic engineering of  Polygonatum cyrtonema  Hua to raise major active ingredient content. Up to now, the transcript sequences are available for different tissues of  P. cyrtonema , a wide range scanning about temporal transcript at different ages’ rhizomes was still absent in  P. cyrtonema . Results Transcriptome sequencing for rhizomes at different ages was performed. Sixty-two thousand six hundred thirty-five unigenes were generated by assembling transcripts from all samples. A total of 89 unigenes encoding key enzymes involved in polysaccharide biosynthesis and 56 unigenes encoding key enzymes involved in saponin biosynthesis. The content of total polysaccharide and total saponin was positively correlated with the expression patterns of mannose-6-phosphate isomerase ( MPI ), GDP-L-fucose synthase ( TSTA3 ), UDP-apiose/xylose synthase ( AXS ), UDP-glucose 6-dehydrogenase ( UGDH ), Hydroxymethylglutaryl CoA synthase ( HMGS ), Mevalonate kinase ( MVK ), 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase ( ispF ), (E)-4-hydroxy-3-methylbut-2-enyl-diphosphate synthase ( ispG ), 4-hydroxy-3-methylbut-2-enyl diphosphate reductase ( ispH ), Farnesyl diphosphate synthase ( FPPS ). Finally, a number of key genes were selected and quantitative real-time PCR were performed to validate the transcriptome analysis results. Conclusions These results create the link between polysaccharides and saponin biosynthesis and gene expression, provide insight for underlying key active substances, and reveal novel candidate genes including TFs that are worth further exploration for their functions and values.

De novo assembly and analysis of Polygonatum cyrtonema Hua and identification of genes involved in polysaccharide and saponin biosynthesis