## 2 Results
### Functional Annotation of the Transcriptome  
Distinct gene sequences were searched using BLAST with a cutoff E-value of 10\({}^{-5}\) against public databases, including Nr, KEGG, COG, and SWISS-PROT. A total of 47,184 unigenes (40.6%) returned a significant Blast result through this approach. Among the 116,214 unigenes, approximately 11,079 (9.5%) showed significant matches with the Nr database. A total of 1082; 1816; and 684 unigenes had significant matches with the KEGG, COG, and SWISS-PROT databases, respectively (Supplementary Figure S1).  
GO assignments were used to classify the functions of the predicted _P. notoginseng_ genes (Supplementary Figure S2A). A total of 367,640 sequences could be categorized into three major GO categories based on sequence homology, namely, biological process, cellular component, and molecular function. They were then classified into 55 functional groups. Cellular, metabolic, and single-organism processes were the most abundant GO terms in the biological process category. Cell and cell part were the most highly dominant terms in the cellular component category. Binding and catalytic activity were the most highly represented terms in the molecular function category. In addition, 35,921 sequences were annotated as a metabolic process category, suggesting that these genes were involved in the metabolite synthesis pathways.  
All the unigenes obtained in the present study were subjected to a search against the COG database to predict and classify the possible functions of transcripts (Supplementary Figure S2B). A total of 90,920 unigenes were clustered into 25 function categories. Among the different COG classes, the major COG category was \"general functional prediction only\" (15,129), followed by \"transcription\" (8430), \"replication, recombination, and repair\" (7715), \"translation, ribosomal structure, and biogenesis\" (6831), \"posttranslational modification, protein turnover, and chaperones\" (6716), and \"signal transduction mechanisms\" (6305). The least-represented groups were \"nuclear structure\" (100) and \"extracellular structures\" (22). Interestingly, our dataset showed that 2233 uni-transcripts annotated with the COG database represented the \"secondary metabolite biosynthesis, transport, and catabolism\" category, indicating that a large number of secondary metabolites existed in _P. notoginseng_.  
The annotated sequences were also mapped to the KEGG to identify the biological pathways of _P. notoginseng_ (Figure 2). As a result, 93,620 sequences were assigned to 21 KEGG pathways. The pathways with the most represented sequences were metabolism, followed by genetic information processing, cellular process, environmental information processing, organismal system, and human diseases. A total of 55,205 sequences were assigned to the metabolic pathways, including global and overview maps (21,073), carbohydrate metabolism (7938), lipid metabolism (4696), and amino acid metabolism (4643). Furthermore, a total of 2128 sequences were annotated to the metabolism of terpenoids and polyketides. These annotations provided useful information to investigate the specific functions and pathways in _P. notoginseng_.  
\begin{table}
\begin{tabular}{c c} \hline \hline
**Item** & **No. of Sequences** \\ \hline Clean reads (M) & 804.6882 \\ clean bases (G) & 120.7032 \\ No. Of contig \textgreater{} 500 bp & 1,325,735 \\ Total unigenes & 158,551 \\ Total length (bp) & 202,104,779 \\ Average contig size (bp) & 1274 \\ N50 contig size (bp) & 2012 \\ GC (\%) & 41.05 \\ \hline \hline \end{tabular}
\end{table}
Table 1: Summary of the transcripts and the assembly results for _P. notoginseng_.