## 2 Results
### RNA-seq-Based Approach for Deciphering Conserved Expressions of Metabolic Enzymes
Expectedly, a sizable percentage of the common DEGs encode for metabolic enzymes (40%), molecular transporters (16%), and transcription factors (5%), among other things (Table S4). To identify the regulation of metabolic enzymes more robustly, gene expressions of the trichomes for various cultivars were then jointly compared with the reference stem sample. As a result, 1031 and 528 genes were broadly identified as being up- and down-regulated in the trichomes, respectively (Figure 1c). Their D-values were generally greater than 1700, while their M-values were smaller or greater than \(-1.6\) and \(1.6\), respectively (Figure 1d; Table S5). Transcriptional Regulation of the Central Metabolism in Trichomes for Enhancing Carbon Feedback Production  
Differential gene expression statistics were then mapped to the metabolic pathways to examine the likely effects of their transcriptional regulation on cannabinoid and terpenoid production. Most gene expression encoding enzymes in the central metabolism were upregulated, as exemplified by the disproportionately larger number of positive M-values compared to negative ones (Figure 2a). Upon further analysis, the glycolytic pathway in the trichomes was found to be re-routed in a consequential manner compared to the stem, due to a significant increase in the expression of specific genes (Figure 2b). For example, \begin{table}
\begin{tabular}{c c c c c c c} \hline \hline \multirow{2}{*}{**Tissue**} & \multirow{2}{*}{**Cultivar**} & **Raw** & **Reads** & **Mapped** & **\% Raw** & **\% Raw** & **Reads after** \\  & & **Reads** & **after QC** & **Reads** & **Reads** & **Further** \\  & & **(mil)** & **(mil)** & **(mil)** & **after QC** & **Mapping** \\ \hline Stem & HB & 248 & 228 & 200 & 92\% & 88\% \\ Trichome & CD & 273 & 261 & 227 & 96\% & 87\% \\ Trichome & GT & 256 & 249 & 215 & 97\% & 86\% \\ Trichome & HB & 260 & 251 & 215 & 97\% & 86\% \\ Trichome & TH & 273 & 262 & 229 & 96\% & 87\% \\ Trichome & WS & 277 & 267 & 235 & 96\% & 88\% \\ \hline \hline \end{tabular}
\end{table} 
Table 1: RNA-seq read statistics. the genome-wide expression of genes encoding the glucose-6-phosphate isomerase (GPI) enzyme increased by 73% overall (D = 2.09 \(\times\) 10\({}^{4}\), Table S6), thus allowing more glucose to be channeled into the pathway. In addition, a 154% net increase in the gene expression for fructose-bisphosphate aldolase (ALDO, D = 3.71 \(\times\) 10\({}^{5}\), Table S6) implied a markedly enhanced availability of G3P metabolites to the MEP pathway for cannabinoid and terpene production. G3P can also be used to produce more NADPH via higher expression of the gene encoding the glyceraldehyde-3-phosphate dehydrogenase [NADP+] (GAPN) enzyme (log\({}_{2}\)FC = 2, D = 1.23 \(\times\) 10\({}^{4}\)) to meet the increased demand of the cofactors during secondary metabolite production (Figure 2b). The enhanced expression of \(GAPN\) in the trichomes has been verified by qPCR (Figure S3). On the other hand, the alternative production of NADH and ATP using G3P, through the action of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and phosphoglycerate kinase (PGK), was found to be suppressed by the down-regulation of the PGK-encoding gene in the trichomes (Figure 2b). This suggests a shift from NADH and ATP production to that of NADPH in the trichomes to support secondary metabolism. Besides G3P and NADPH, pyruvate formation was also found to be promoted in the trichomes. There was a significantly higher expression of genes for pyruvate kinase (PK) enzymes (Figure 2b) that produce pyruvate, with an overall 78% increase in expression (D = 7.69 \(\times\) 10\({}^{4}\), Table S6). In further coordination, the phosphoenolpyruvate carboxylase (PEPC) enzyme was also down-regulated (log\({}_{2}\)FC = \(-\)1.9, D = 1.99 \(\times\) 10\({}^{4}\)) to redirect phosphoenolpyruvate to pyruvate conversion, instead of oxaloacetate production. Pyruvate is also used as a substrate for forming acetyl coenzyme A (AcCoA) via pyruvate dehydrogenase (PDH) reactions [24].