## 3 Results
### KEGG Enrichment and Mapman Analysis of DEGs in Rosemary Suspension Cells
(**A**) heat map of the expression of DEGs in phenylpropanol biosynthesis. (**B**) simplified diagram of phenylpropanol and flavonoid biosynthetic pathway. (**C**) heat map of the expression of DEGs in flavonoid biosynthesis. thesis (Figure 5B). Among these DEGs, these were 14 DEGs drastically up-regulated under different concentrations of MeJA treatments, include 1 _CHS_, 1 _CHI_, 1 _F3H_, 2 _FLS_, 4 _ANS_, 1 _GTI_, 1 _HIDH_, 1 _IF7 GT_, 1 _CYP81E1/E7_, 1 _UGT73C6_. Instead, these were 5 DEGs drastically down-regulated from 0 to 100 \(\upmu\)M MeJA treatment, include 1 _F3H_, 1 _DFR_, 1 _3 AT_, 1 _IF7 MAT_ and 1 _UGT73C6_. The other 16 DEGs showed different differential expression patterns under different concentrations of MeJA, most of the DEGs were up-regulated under 10 \(\upmu\)M MeJA treatment, but down-regulated under 50 and 100 \(\upmu\)M MeJA treatment, for example, _CHI_ (Unigene14082_All), which was down-regulated more significant under 100 than 50 \(\upmu\)M MeJA treatment (Figure 5C). Therefore, indicating that different concentrations of MeJA could significantly affect the accumulation of flavonoids in rosmenary suspension cells. Terpenoid Biosynthesis Related Genes Were Differential Expressed during Rosemary Suspension Cells under Different Concentrations of MeJA  
In our study, the results showed that a large number of DEGs were found in the terpenoid biosynthesis and terpenoids biosynthesis pathways (Figure 6). There were 6 significant DEGs assigned to the MVA pathway, including 1 _HMGCS_, 3 _HMGCR_, 1 _MVK_, and 1 _PMVK_. Among these DEGs except _HMGCS_ (CL375.Contig4_All) and _HMGCR_ (Unigene29235_All, CL6936.Contig10_All) were drastically up-regulated under different concentrations of MeJA treatments. There were 3 significant DEGs that were assigned to the MEP pathway, including 2 _DXS_ and 1 _ispH_. _DXS_ were down-regulated under 10 \(\upmu\)M MeJA treatment, but up-regulated under 50 and 100 \(\upmu\)M MeJA treatments, ispH was drastically down-regulated under different concentrations of MeJA treatments. The result showed that 100 \(\upmu\)M MeJA treatment could significantly induce the DEGs expression of MVA biosynthesis compared to 50 and 100 \(\upmu\)M MeJA, 10 \(\upmu\)M MeJA treatment could significantly inhibit the DEGs expression of MVA biosynthesis in rosmenary suspension cells. In addition, the DEGs _FPS_ (_FDPS_) and _GGPS_, which directly act on terpenoids to synthesize precursors geranyl diphosphate (GPP), farnesyl pyrophosphate (FPP) and geranyl pyrophosphate (GGPP) and other DEGs in the terpenoid biosynthesis pathway showed differential expression patterns under different concentrations of MeJA, for example _FDPS_ (CL1142.Contig2_All, Unigene14392_All), _GGPS_, _FACE2_, _ICMT_, _PCME_ (Unigene7748_All) and _FOLK_ were up-regulated from 0 to 100 \(\upmu\)M MeJA treatment. We also found a large number of DEGs were assigned to ubiquinone and other terpenoid-quinone biosynthesis, carotenoid biosynthesis, sesquiterpenenoid and triterpenoid biosynthesis, zeatin biosynthesis, steroid biosynthesis, monoterpenoid biosynthesis and N-Glycan biosynthesis pathways (Figure S9). Therefore, different concentrations of MeJA could significantly affect the accumulation of terpenoids in rosmenary suspension cells. Transcription Factors Are Important in Rosemary Suspension Cells under Different Concentrations of MeJA  
In this study, a total of 551 TFs were annotated, belonging to 43 TFs families in rosmenary suspension cells (Figure 7A). Under the MeJA treatments, many differentially expressed TFs were found (Figure 7B,C). For example, MYB (15.97%), AP2-EREBP (14.88%), bHLH (8.17%), NAC (7.62%), WRKY (5.63%), G2-like (4.54%), C2H2 (4.54%), MADS (3.45%), Tify (3.09%), C3H (2.90%) and LOB (2.90%) which frequency were more than 2.90%, indicating that these TFs might play important regulatory roles in the synthesis of rosmenary suspension cells important metabolites and the stress-response.