## 2 Results
### Integrated Analysis of Transcriptome and Proteome
Accordingly, the expression levels of genes related to chlorophyll biosynthesis, including porphobilinogen synthase (_HemB_), protoporphyrinogen/coproporphyrinogen III oxidase (_HemY_), and magnesium-protoporphyrin O-methyltransferasease (_chlM_), were notably elevated. Consistently, the expression levels of genes associated with terpenoid biosynthesis were also greatly elevated, including MVA pathway-related genes like farnesyl diphosphate synthase (_FPPS_), MEP pathway-related genes like geranyl diphosphate synthases(_GPPS1_ and _GPPS2_), and monoterpene synthase-like beta-pinene synthase (_MonoTPS2_). In addition, sucrose-phosphate synthase (_SPS_) referred to as sucrose biosynthesis and 6-phosphofructokinase (_PFK_) referred to as glycolysis were also dramatically up-regulated. Interestingly, several genes related to circadian rhythm-plant, including phytochrome-interacting factor 3 (_PIF3_), casein kinase II subunit alpha (_CSNKA2_), cryptochrome 1 (_CRY1_), and transcription factor HY5 (_HY5_), were obviously up-regulated (Table S3). On the contrary, the expression levels of genes involved in phenylpropanol biosynthesis significantly declined, including phenylalanine ammonia-lyase (_PAL_), 4-comarate-CoA ligase (_4 CL_), and caffe acid 3-O-methyltransferaseas (_COMT_). Consistently, the expression levels of genes that participated in flavonoid biosynthesis, including chalcone synthase (_CHS_), flavonoid synthase (_FLS_), _DFR_, _ANS_, and _ANR_, were greatly downregulated. Besides, GA biosynthesis genes including ent-copalyl diphosphate synthase 1 (_CPS1_) and ent-kaurene oxidase 1 (_KO1_) as well as JA signaling genes including three coronate-insensitive proteins 1 (_CO1s_) and two jasmonate ZIM domain-containing protein (_JAZs_) were significantly down-regulated (Table S3). There were 542 up-regulated and 443 down-regulated DEPs whose corresponding genes were not differentially expressed (Figure S4). As expected, proteins involved in the MEP pathway were significantly up-regulated, including 1-deoxy-D-xylulose 5-phosphate reductoisomerase (DXR), 4-diphosphocytidyl-2-C-methyl-D-erythitol kinase (CMK), 2-C-methyl-D-erythitol 2,4-cyclodiphosphate synthase (MDS), 4-hydroxy-3-methylbut-2-en-1  
Figure 6: Functional category enrichment of DEGs/DEPs. DEGs/DEPs were classified into a total of 6 groups according to RNA-Seq and iTRAQ integrative analysis. The degree of the pathway enrichment was indicated according to the value of \(-\)log(\(q\)-value), as shown in the color bar. Each group was indicated by expression level (“go” for gene only, “po” for protein only, and “gp” for both gene and protein level, respectively) and regulatory direction (“up” for up-regulated and “dn” for down-regulated, respectively). The color brightness represents the degree of significant enrichment of pathways, as shown in the color bar. yl diphosphate reductase (HDR1), and geranylgeranyl diphosphate synthase (GGPPS1). Accordingly, proteins related to terpenoid biosynthesis were greatly up-regulated, including monoterpenoid biosynthesis-related proteins like alpha-pinene synthase (MonoTPS3), diterpenoid biosynthesis-related proteins like monofunctional isopimaraadiene synthase (DiTPS), and diterpene resin acid biosynthesis-related proteins like cytochrome P450 720 Bs (CYP720B8, CYP720B10, and CYP720B11). Consistent with the MEP pathway, proteins associated with photosynthesis were dramatically up-regulated as well, including photosystem I subunit PasKa, and photosystem II protein Psb28, rbc5, ribulose-1,5-bisphosphate carboxy-lase/oxygenase large subunit (rbcL) and glyceraldehyde 3-phosphate dehydrogenase A subunit (GAPA). Similarly, many proteins that participated in aminoacyl-tRNA biosynthesis were also notably up-regulated.