## 3 Discussion
They then collected 10 root samples from SP (five stages) and FP (five stages) and mixed them together to construct a root transcriptome library, collected 10 leaf samples to construct a leaf transcriptome library, and obtained 71,922 and 54,722 unigenes from the mixed root and mixed leaf libraries via the Illumina HiSeq(tm) 2500 system, respectively [43]. [PERSON] et al. generated a total of 81,003 unique sequences from the cDNA library constructed from the ARs, TARs, and DTRs of _R. glutinosa_ by using the Illumina sequencing platform [41]. In this study, we obtained 38,678-54,378 unigenes from the 24 cDNA libraries of radial striations and non-radial striations of _R. glutinosa_ tuberous roots and eventually assembled a final set of 150,405 entries with an average length of 1244 bp higher than mixed roots unigenes (383 bp and 678 bp) [17; 41] and mixed leaf and root unigenes (868 bp) [43]. This novel unigene database provides a high-quality reference transcriptome on gene expression detection and molecular mechanisms for _R. glutinosa_. Gene expression analysis has been extensively utilized for the identification of enzyme genes involved in secondary metabolites biosynthesis by measuring transcriptional levels in different tissues and developmental stages. Phytochemical analysis of the peeled _Salvia milliorrhiza_ root tissues demonstrated the localization of tanshinones in the periderm, and transcriptome analysis revealed that the two key enzyme coding genes _SmCPS1_ and _SmKSL1_ were specifically expressed in the periderm [7]. Lithospermic acid B accumulates in the phloem and xylem of _S. miliiorrhiza_ roots, in agreement with the expression patterns of the identified key genes, including _SmRAS_, _SmC4H1_, and _SmCYP98A78_, related to rosmarinic acid biosynthesis [8]. We identified 155 transcripts (encoding 14 enzymes) involved in the iridoid glycoside biosynthesis pathway from this _R. glutinosa_ unigene database. The expression patterns of _Unigene66333_ (IPI) and _Unigene34693_ (CPM) could match the change in catalpol content and were considered to be the better candidate genes for catalpol biosynthesis. Among the 223 unigenes encoding nine enzymes involved in acteoside biosynthesis, the expression levels of _CL7017.Contig3_ (PPO) and _CL4500.Contig3_ (TyDC) in different tuberous root tissues were similar to content changes in acteoside and total phenylethanol glycosides. Furthermore, _CL4500.Contig3_ (TyDC) was considered to be the best candidate for acteoside synthesis. Glycosyltransferase (GTs) comprise a ubiquitous family of enzymes that catalyze the transfer of a sugar moiety from an activated donor molecule onto saccharide or non-saccharide acceptors, resulting in the formation of various glycosides of non-carbohydrate moieties [44], which play important roles in acteoside and catalpol biosynthesis. In total, 325 UGTs were identified in this report. Transcriptome analysis showed that three members of UGTs, including _CL3773.Contig3_, _CL5268.Contig2_, and _Unigene12367_, were upregulated in non-radial striations for every cultivar. Furthermore, _CL10318.Contig4_ and _CL11397.Contig2_ indicated higher expression levels in non-radial striation of BJ1 and QH, which is consistent with the change in catalpol accumulation, possibly involved in catalpol synthesis. Over the past decade, TFs have been key regulators in controlling gene expression by binding to the promoter of single or multiple genes. Many experiments have confirmed that TFs are involved in the biosynthesis of various secondary metabolites in plants [30; 45; 46]. Two bHLH family genes, _TSAR1_ (Triterpene Saponin biosynthesis Activating Regulator1) and _TSAR2_, regulate triterpene saponin biosynthesis in _Medicago truncatula_[47]. Overexpression and RNAi transient assays revealed that the two MYB transcription factors (_bMYB10b_ and _PbMYB9_) regulate flavonoid biosynthesis in _Pyrus bretschneideri_ fruit [30].