## 2 Comparative Transcriptome Provides Informative Data in Biosynthetic Pathway Analysis  
Advances in sequencing and bioinformatics analysis could provide a large amount of candidate genes for the biosynthetic pathway responsible for the secondary metabolites. _S. miliorrhiza_ hairy root could be generated by infecting leaf explants with _Agrobacteriumrium rhizogenes_ strains in _S. miliorrhiza_[19,20] and exhibits a similar protective activity against hypoxia and reoxygenation injury in rat cardiac myocytes to _danshen_[21]. In addition, the secondary metabolites in hairy roots could be stimulated by elicitorswithin several days, which provide a simplified system to identity new candidate genes by different expression or comparative transcriptome analysis. The first cDNA microarray analysis for different stages of _S. miltiorrhiza_ hairy root cultures revealed 203 differentially expressed genes from 4354 cDNA clones, including seven genes (especially two important terpenoid synthases) involved in tanshinone biosynthesis [22]. However, the information in cDNA microarray is limited, a large amount of candidates related to the post-modification progress in biosynthesis of secondary metabolites are to be investigated. Deep sequencing could provide high-throughput data for the discovery of candidate genes involved in the biosynthesis of natural products, especially in non-model species. Furthermore, comparative transcriptome analyses of different tissues with and without active ingredients could provide a comprehensive insight into the biosynthesis and regulation of these compounds. In the transcriptome over the entire growth cycle, including the seedling stage, vegetable stage, and different tissues in the reproductive stage, a total of 47 unigenes encoding more than 24 enzymes and 200 unigenes related to 32 enzymes were identified, which are potentially involved in the biosynthesis of rosmarinic acids and terpenoids, respectively[23]. In a more recent study, [PERSON] _et al._ further conducted transcriptomic profiling of the _S. miltiorrhiza_ root and leaf tissues by using 454 GS-FLX pyrosequencing platform to identify genes and transcriptional regulators involved in the biosynthesis of tanshinones. 168 unigenes involved in the biosynthesis of the terpenoid backbone and 2863 unigenes that are highly expressed in roots were identified, including those genes involved in the biosynthesis of tanshinones, such as copalyl diphosphate synthase (_SmCPSI_), kaurene synthase-like (_SmKSLI_) and _CYP76 AH1_[24]. The transcriptome among different tissues including different expression genes related to plant development resulted in too many candidates for further characterization, while the comparative transcriptome from different elicitation processes could significantly narrow the candidates for functional characterization. The transcriptional profiles of MJ elicitated _S. miltiorrhiza_ leaves yielded 37647 unique sequences. Almost all of the known genes involved in tanshinone and phenolic acid biosynthesis in _S. miltiorrhiza_ were expressed differentially between the untreated and treated samples. Three and four candidate P450s that could be involved in the biosynthesis of tanshinones and phenolic acids, respectively, were selected from the RNA-seq data based on the co-expression analyses with _SmCPSI/SmKSL1_ or _SmRAS_[25]. Metabolomics could further provide an instantaneous snapshot of the entire physiology of an organism by comparing the relative differences between biological samples based on their metabolite profiles. [PERSON] _et al._ combined metabolomics and deep sequencing to investigate the inducible biosynthesis of tanshinones. The comprehensive transcriptome comprised 20972 non-redundant genes, of which 39 CYPs exhibited up-regulation at all time points following induction. Eight cytochrome P450s (P450s) were co-regulated with known genes involved in tanshinones biosynthesis, providing targets for future investigations [26].