## 2 Results and Discussion
### Gene Function Annotation and Classification
A high affinity nitrate transporter [36] was eight-fold higher in roots than in leaves. In higher plants, there are two nitrate uptake systems, the high and low affinity transporter systems, and the high affinity nitrate transporter functions when the nitrate concentration is low [37; 38]. Putative Genes Involved in the Terpenoid Backbone Biosynthesis and Gentiopicroside Biosynthetic Pathways  
Terepenoids, including monoterpenoids, triterpenoids, chlorophyls, carotenoids, abscisic acid, cytokinin gibberellins, sterols, sesquiterpenoids, and ubiquinones, are all closely related with the terpenoid backbone biosynthesis [39; 40]. The terpenoid backbone is derived from the universal precursor, isopentenyl diphosphate (IPP), and its allylic isomer, dimethylallyl diphosphate (DMAPP), which are derived from the mevalonate (MVA) and/or the methylerythnitol phosphate (MEP) pathways [41] (Figure S1). Transcripts encoding the enzymes involved in the MVA and MEP pathways were searched against the unigenes and transcripts present in our database (Table 4). In general, transcripts of MVA and MEP pathway genes were more abundant in leaves, as revealed by much higher numbers of reads of 3-hydroxy-3-methylglutaryl-CoA reductase (_GrHMGR_), 5-diphosphonate decarboxylase (_GrMVD_), Isopentenyl diphosphate isomerase (_GrIDI_), 1-deoxy-Dxylulose 5-phosphate synthase (_GrDXS_), 1-deoxy-D-xylulose-5-phosphate reductio isomerase (_GrDXR_), 2-\(C\)-methyl-l-erythnitol 2,4-cyclodiphosphate synthase (_GrMCS_), and 4-hydroxy-3-methylbut-2-enyl diphosphate synthase (_GrHDS_) genes in leaves than in roots (Table 5, Figure S2). qRT-PCR (quantitative Reverse Transcription-Polymerase Chain Reaction) results showed that the selected genes _GrDXS1_, _GrHDS_, and _GrIDI1_ were more abundant in leaves (Figure 8). These results support the observation that gentiopicroside is synthesized in shoots and allocated to the roots [6]. \begin{table}
\begin{tabular}{c c c c c} \hline
**Pathway** & **Gene Name** & **Unigene** & **RPKM in Leaf** & **RPKM in Root** \\ \hline _AACT1_ & comp81670\_c0 & 50.65 & 52.76 \\ _AACT2_ & comp86403\_c0 & 13.16 & 38.43 \\ _HMGS_ & comp1196622\_c0 & 0.00 & 0.49 \\ _HMGR1_ & comp87249\_c0 & 27.14 & 3.53 \\ _HMGR2_ & comp92954\_c0 & 35.56 & 17.08 \\ _HMGR3_ & comp4296\_c0 & 0.25 & 0.57 \\ _HMGR4_ & comp25979\_c0 & 0.57 & 0.04 \\ _HMGR5_ & comp114241\_c0 & 5.72 & 0.00 \\ _MK_ & comp83300\_c0 & 20.74 & 16.19 \\ _PMK1_ & comp371052\_c0 & 0.55 & 0.48 \\ _PMK2_ & comp82309\_c1 & 2.21 & 1.23 \\ _PMK3_ & comp82309\_c0 & 3.94 & 2.21 \\ _PMK4_ & comp92698\_c0 & 8.08 & 11.20 \\ _MVD1_ & comp86107\_c0 & 51.01 & 39.76 \\ _MVD2_ & comp73189\_c0 & 0.55 & 0.58 \\ _IDI1_ & comp81822\_c0 & 114.79 & 89.95 \\ \hline \end{tabular}
\end{table} 
Table 4: Expression of putative genes in MVA and MEP biosynthesis pathways. \begin{table}
\begin{tabular}{c c c c c} \hline
**Pathway** & **Gene Name** & **Unigene** & **RPKM in Leaf** & **RPKM in Root** \\ \hline \multirow{3}{*}{MVA} & _ID12_ & comp67360\_c0 & 37.65 & 31.50 \\  & _ID3_ & comp92050\_c0 & 49.18 & 2.79 \\ \hline \multirow{9}{*}{MEEP} & _DXS1_* & comp87916\_c0 & 45.34 & 1.45 \\  & _DXS2_ & comp89290\_c0 & 10.85 & 3.64 \\  & _DXS3_ & comp93517\_c0 & 48.69 & 35.56 \\  & _DXR_ & comp92087\_c3 & 123.96 & 107.04 \\  & _MCT_ & comp67067\_c0 & 36.76 & 8.28 \\  & _MCS_ & comp91375\_c0 & 56.61 & 36.13 \\  & _HDS_* & comp94424\_c0 & 151.28 & 77.99 \\  & _HDR1_ & comp87777\_c0 & 114.07 & 97.97 \\  & _HDR2_ & comp509208\_c0 & 0.00 & 0.91 \\  & _HDR3_ & comp1116482 c0 & 0.00 & 0.36 \\ \hline \end{tabular}
* These genes were selected for qRT-PCR.  
\end{table} 
Table 4: _Cont._