## 2 Results and Discussion
### Expression Patterns of Four Short-Chain Prenyltransferase _Genes_  
In nature, terpenoid biosynthesis is regulated at multiple metabolic branch points to create large structurally and functionally diverse compounds [40, 41]. The so called \"short-chain prenyltransferases\", _i.e.,_ the enzymes geranyl diphosphate synthase (GPPS), FPPS and GGPPS that catalyze the condensations of IPP and DMAPP to geranyl diphosphate (GPP), FPP and GGPP respectively, are situated at the primary branch point of the central terpenoid pathway, directing carbon flux into different classes of terpenoids and so in control of the product distribution [41]. GPP is the entry point leading to the biosynthesis of all monoterenoid products; FPP is a key precursor in the formation of sesquiterpenoids and triterpenoids and in the biosynthesis of sterols, brassinosteroids and ubiquinones; while GGPP is a central precursor for a diverse group of primary and specialized terpenoid compounds such as carotenoids, chlorophylls, ABA, gibberellins and diterpenoids [42]. As described above, GPPS is the key branchpoint enzyme leading to monoterpene biosynthesis, so it is valuable to discover _R. glutinosa_ GPPS genes and gain an insight into their molecular characters. Among the terpenoid biosynthetic genes identified in this study, we found two sequences whose encoding proteins have high similarities to the _Antirrhinum majus_ GPPS large subunit (GPP.LSU), sharing 95% (63/66, ratio of identical amino acids) and 92% (35/38) sequence identities, respectively, which are very likely to belong to the same gene, because they correspond to one unigene. Apart from these, no other putative gene encoding GPPS was discovered. In comparison, the transcripts that were predicated to be _FPPSs_ and _GGPPSs_ were much more abundant. GPPSs can exist as heterodimer or homodimeric proteins. In the heterodimer enzymes, the catalytic GPP.LSU had high amino acid sequence identity to plant GGPPSs, whereas the sequence of the noncatalytic smaller subunit (GPPS.SSU) is related to, but much more divergent from, the sequences of GGPPSs; GPP.LSU can be either an active GGPPS or an inactive GGPPS-like protein, it is the GPP.SSU that determines the product specificity of the catalytic large subunit [43, 44, 45, 46]. It had been further shown that GPP.SSU can bind to a variety of bona fide GGPPS enzymes (_i.e._, GGPPSs from _Taxus canadensis_, _Abies grandis_ and _Nicotiana tabacum_) to form an active heterodimeric enzyme catalyzing GPP formation [43, 46]; even heteroexpression of _A. majus_ GPS.SSU in tobacco resulted in an increase of monoterpenoids and drastic effects due to deficiency of GGPP [46]. It is not surprising that plant GGPPSs can serve as the catalytic subunits of GPPS, because the short-chain prenyltransferase, excepting GPPS.SSUs, show a high level sequence similarity to one another, some of which tend to display dual (or adventitious) activities, producing products with more or fewer C5 (IPP) unit(s) than the main product [47]. For example, the homodimeric PaIDS1 which has strong sequence identity to other conifer GPPSs and GGPPSs is a bifunctional GPP/GGPP synthase, whose catalytic properties and reaction mechanism resemble those of conifer GGPPS, except that significant quantities of the intermediate GPP are released [48]. Since no other form of GPPS had been discovered, it seemed that it is the heterodimer GPPS that is responsible for the formation of GPP in tuberous of _R. glutinosa_. Only a few GPPS.SSUs have been characterized, and due to the divergence of their sequences [45], we cannot identify a GPPS.SSU homologue from the 454 assembly. As mentioned above, a hetero-GPPS.SSU can interact with endogenous GGPPSs and form functional GPPSs. However, whether _R. glutinosa_ has only specific genes for GPPS.LSU, or it can also recruit GGPPS genes for this purpose, has yet to be determined. A comparative analysis of gene expression profiles would be helpful for understanding their roles in this plant.