## 3 Results
### Combined Analysis of Transcriptome and Metabolome  
Integrated analysis indicated that 17 DEGs and four DMs participated in four KEGG reference pathways together, including phenylpropanol biosynthesis and the alpha-linonic acid metabolism pathway (Table S4). In the phenylpropanol biosynthesis, one DM (eugenol) and nine DEGs (_PAL_, _C4H_, _4 CL_, _POX_, _CCR_, _CAD_, _TOGT_, _COMT_, and _CCoAOMT_) were mapped together, and there was a high correlation between eugenol and _PAL_, _C4H_, _4 CL_, _CCR_, _CAD_, _COMT_, and _CCoAOMT_. In addition, DMs (_Z_)-3-hexenal and six DEGs (_LOX_, _AOS_, _AOC_, _OPR_, _ACAA_, _MFP_2) were mapped to the alpha-linonic acid metabolism pathway. Here, a strong correlation between (Z)-3-hexenal and _LOX_ existed (Figure 7).  
Figure 5: Statistics of KEGG pathway enrichment of DEGs. Rich factor represents the ratio of the number of DEGs enriched into the pathway to the total number of genes annotated into the pathway.  
Figure 6: A comparison of differential expressed genes related to floral scent in flowers by RNA-seq and real-time PCR. Limonene and pinene degradation: ECHS, enoyl-CoA hydratase. Terpenoid backbone biosynthesis: GPPS, geranyl diphosphate synthase; FLDH, NAD\({}^{+}\)-dependent farnesol dehydrogenase.henylpropanol biosynthesis: PAL, phenylalanine ammonia-lysse; C4H, cinnamate 4-monooxygenase; POX, peroxidase; CAD, cinnamyl-alcohol dehydrogenase; CCR, cinnamoyl-CoA reductase; TOGT, scopoletion glucosyltransferase. alpha-Linolenic acid metabolism: LOX, lipoxygenase; AOC, allene oxide cyclase; ACAA, acetyl-CoA acyltransferase.  
In the phenylpropanol biosynthesis pathway, the relative content of eugenol in TH was much higher than that in TL, and its major regulatory genes located in the downstream and alternative pathways showed the same tendency, such as _CCR_, _CCoAOMT_, and _COMT_. However, the main upstream structural genes associated with eugenol biosynthesis showed decreasing tendency compared with TL, including the significant members in the common phenylpropanol pathway, such as _PAL_, _C4H_, and _4 CL_. In order to study the screened structural genes related to the eugenol synthesis, expression analysis by qRT-PCR was performed on _PAL_ and _C4H_ in the three flowering stages of high-scent \(D\). _loddigesii_, and the results showed that the expression level of _PAL_ was the lowest in the blooming period, and the expression level of _PAL_ was higher, but it was not significantly differentiated between the other two flowering periods; _C4H_ has the highest expression in the bud stage and shows the lowest expression in the blooming period (Figure 8). The biosynthesis of (Z)-3-hexenal was relatively simple, the relative content of (Z)-3-hexenal and the expression of its upstream structural gene _LOX_ both showed a downward trend in TH.  
Figure 8: Expression patterns of _PAL_ and _C4H_ at three different flowering period in high-scent \(D\). _loddigesii_.  
Figure 7: Change fold of DEGs and DMs in TH compared to TL. (**a**) Phenylpropanol biosynthesis: 4 CL, 4-coumaroyl-CoA ligase; C3H, _p_-coumarate-3-hydroxylase; COMT, caffeic acid O-methyltransferase; cocoAOMT, caffeoyl-CoA O-methyltransferaseerase; CFAT, coniferyl alcohol acetaryl-transferase; EGS, eugenol synthase; (**b**) alpha-Linolenic acid metabolism: HPL, hydroperoxide lyase; 13(S)HpOTrE, (92,11E,152)-(138)-Hydroperoxyoctadeca-9,11,15-trienoate. Other abbreviations were as shown in Figure 4. Red represented the mapped DEGs and DMs. Dotted arrow represented unknown steps; double arrows represented multiple steps.