G.pentaphyllum(Gynostemma Pentaphyllum)a creeping herbaceous perennial with much important pharmacological functions,is widely distributed in Asia.Gypenosides,the main effective component of G.pentaphyllum,are well-studied in published researches.FPS(Farnesyl Pyrophosphate Synthase),SS(Squalene Synthase),and SE(Squalene Epoxidase)are the main enzymes involved in the synthesis of Gypenosides.It is necessary to investigate the transcriptomic information of G.pentaphyllum to facilitate future studies of transcriptional regulation.We assembled the original reads and obtained 50,654,708 unigenes based on RNA-sequencing the fibrous roots,stems,and leaves of G.pentaphyllum.Finally,we noticed FPS,SS,and SE showed differential expression of enzymes in DESeq.Although the leaves were the sample with lowest unigenes expression in overview,leaves showed the highest expression of FPS,SS and SE which was consisted to the distribution of gypenosides content.Moreover,several sequences with high similarity with the “bitterness sequences” of cucumber were found in our study which may reveal the reason why the taste of G.pentaphyllum were differed from the strains.For FPS,SS and SE of G.pentaphyllum,our article is the first report to analyze the association among the expression of these enzymes,unigenes and the content of their production.Future studies of transcriptional regulation on gypenosides of G.pentaphyllum should be taken to explore the mechanisms of synthesis and regulation of gypenosides.