## 5 Conclusions  
In this study, we performed the transcriptome analysis of leaf, stem and root tissues in _C. chinense_, and identified numerous genes related to triterpen saponin biosynthesis using RNA-seq sequencing. A few genes encoding key enzymes were validated by qRT-PCR and the results were well in accordance with the expression data obtained by RNA-seq sequencing. This study will be useful to support our understanding of the mechanism of triterpen saponin biosynthesis in _C. chinense_ at the molecular level. It could also greatly assist the research in molecular biology and mass production of triterpen saponins.  
Supplementary Materials: Supplementary materials can be found at [[http://www.mdpi.com/1422-0067/20/11/2643/s1](http://www.mdpi.com/1422-0067/20/11/2643/s1)]([http://www.mdpi.com/1422-0067/20/11/2643/s1](http://www.mdpi.com/1422-0067/20/11/2643/s1)).  
**Author Contributions:** Project design: J.W.W., D.Y.P. and L.Q.H. Experiments and data analysis: Y.Y.S., S.X.Z., C.K.W., D.R.Z., and K.L.M. Manuscript preparation: Y.Y.S. Preparation of plant materials: Q.S.Y. All the authors read and approved the final manuscript.  
**Funding:** This work was funded by the Project of Sustainable Utilization of Famous Traditional Chinese Medicine Resources (2060302), the National Key Research and Development Plan (2017 YFC1701600), the Natural Science Research Grant of Higher Education of Anhui Province (KJ2018 ZD028), the Natural Science Foundation of Anhui Province of China (1608085 MH177), the National students' platform for Innovation and Entrepreneurship Training Program (201810369050).  
**Conflicts of Interest:** The authors declare no conflicts of interest.  
**Data Availability:** The RNA-seq datasets of three _C. chinense_ tissues were deposited in the NCBI Sequence Read Archive (SRA) database (Accession: SRP166297).  
**Abbreviations**  
AACT Acetyl-CoA C-acetyltransferase  
CAS Cycloartenol synthase  
cDNA Complementary DNA  
CMK 4-diphosphocytidyl-2-C-methyl-D-erythnitol kinase  
DDS Dammarenediol II synthase  
DEGs Differentially expressed genes  
DMAPP Dimethylallyl diphosphate  
DXR 1-deoxy-D-xylulose-5-phosphate reductoisomerase  
DXS 1-deoxy-D-xylulose-5-phosphate synthase  
FC Fold change  
FDR False discovery rate  
FPKM The fragments per kilobase of transcript per Million mapped  
reads  
FPPS Farnesyl-diphosphate synthase  
GO Gene Ontology  
GPPS Geranyl-diphosphate synthase  
GT Glycostransferases  
HDR 4-hydroxy-3-methylbut-2-en-1-yl diphosphate reductase  
HDS (E)-4-hydroxy-3-methylbut-2-enyl-diphosphate synthase  
HMGR Hydroxyplituryl-CoA reductase  
HMGS Hydroxyplituryl-CoA synthase  
IDI Isopentenyl-diphosphate Delta-isomerase  
IPP Isopentenyl pyrophosphate  
LS Lupeol synthase  
LSS Lanosterol synthase  
KEGG Kyoto Encyclopedia of Genes and Genomes  
KOG Clusters of euKaryotic Orthologous Groups  
MCT 2-C-methyl-D-erythnitol 4-phosphate cytidylyltransferase  
MDC Dipphosphonate decarboxylase decarboxylase  
MDS 2-C-methyl-D-erythnitol 2,4-cyclodextrin diphosphate synthase  
MEP 2-C-methyl-D-erythnitol-4-phosphate  
MK Mevalonate kinase  
MVA Mevalonate  
NR NCBI non-redundant protein sequences  
NT NCBI nucleotide sequences  
PDMO Cytochrome P450-dependent monooxygenases  
PlnTFDB Plant transcription factor database  
PMK Phosphomevalonate kinase  
qRT-PCR Quantitative real-time PCR  
SM Squalene monooxygenase  
SS Squalene synthase  
TF Transcriptome factor  
TGICL TGI clustering tool  
\(\alpha\)-AS \(\alpha\)-amyrin synthase  
\(\beta\)-AS \(\beta\)-amyrin synthase