## 3 Results
### KEGG Enrichment and Mapman Analysis of DEGs in Rosemary Suspension Cells
Other DEGs showed different expression patterns in the three combinations (Figure S7A). Meanwhile, we found a total of 25 DEGs were assigned to JA signal transduction, including 2 _JAR1_, 1 _COII_, 9 _JAZ_ and 13 _MYC2_. Only 1 _JAR1_ (Unigene18877_All) was up-regulated under 10 uM MeJA treatment, others were down-regulated. _COII_ was drastically up-regulated from 0 to 100 uM MeJA treatment. _JAZ_ (CL9927.Contig1_All) was down-regulated under 10 uM MeJA treatment, others were up-regulated. 1 _MYC2_ (CL4564.Contig5_All) was down-regulated from 0 to 100 uM MeJA treatment, 6 _MYC2_ (CL2762.Contig2_All, CL4726.Contig3_All, CL7026.Contig2_All, CL9744.Contig1_All, CL12032.Contig4_All, Unigene30434_All) were down-regulated from 0 to 100 uM MeJA treatments, the number of up-regulated DEGs under 100 uM MeJA treatment were the most, secondly was 50 uM MeJA treatment, the least was 10 uM MeJA treatment (Figure S7B). The result showed that 100 uM MeJA treatment can significantly induce the DEGs expression of JA biosynthesis and signal transduction pathway compared to10 and 50 uM MeJA, indicating that 100 uM MeJA could significantly affect JA biosynthesis and signal transduction in rosemary suspension cells. In our study, based on the KEGG and other annotation, plant hormone signal transduction was the representative pathway. There were 248 significant DEGs were assigned to the plant hormone signal transduction pathway involved in auxin (59 DEGs), cytokine (56 DEGs), gibberellin (GA, 34 DEGs), abscisic acid (ABA, 15 DEGs), ethylene (ET, 44 DEGs), brassinosteroid (BR, 32 DEGs), and salicylic acid (SA, 8 DEGs) (Figure S7C-I). The result of the analysis of these DEGs showed that 69 DEGs were up-regulated under different concentrations of MeJA, including 4 _AAIX1_, 3 _TIR1_, 14 _AUX-IAA_, 5 _ARF_ and 8 _TF_, 87 DEGs were down-regulated, for example, 1 _SAUR_, 10 _TF_, 22 _B-ARR_, 4 _A-ARR_, 3 _ABF_, 6 _ETR_ and 3 _CTR1_. The result also showed that 50 and 100 \(\upmu\)M MeJA could significantly inhibit the DEGs expression of the salicylic acid signal transduction pathway (Figure S7C). There were more numbers of up-regulated DEGs in auxin and ABA signal transduction under different concentrations of MeJA (Figure S7D,E), but more numbers of down-regulated DEGs in other hormone signals transduction pathways under different concentrations of MeJA (Figure S7F-I). Phenylpropanoloid Biosynthesis Related Genes Were Differential Expressed during Rosemary Suspension Cells under Different Concentrations of MeJA  
Phenylpropanoloid biosynthesis was the representative KEGG pathway, we found 138, 104 and 138 DEGs assigned to phenylpropanol biosynthesis in CKvsM10, CKvsM50 and CKvsM100 combinations, respectively (Figure 5B). These DEGs include 5 _PAL_, 4 _4 CL_, 8 _CCR_, 6 _HCT_, 8 _C3'H_ (_CYP98A_), 8 _F6H1_, 3 _CSE_, 1 _caffevol-CoA-O-methyltransferasesferase_, 21 _\(\beta\)-glucosidase_, 27 _cinnamyl-alcohol dehydrogenase_, 66 _pexoxidase_. There were more numbers of up-regulated DEGs than down-regulated DEGs under 10 \(\upmu\)M MeJA treatments, but there were more numbers of down-regulated DEGs under 50 and \(\upmu\)M MeJA treatment. Among these DEGs, _PAL_ (CL3764.Contig6_All), 4_CL_ (CL5102.Contig4_All), _CCR_ (Unigene974_All), _HCT_ (CL10076.Contig1_All), _F6H1_ (CL352.Contig1_All), peroxidase (Unigene16028_All), _\(\beta\)-glucosidase_ (CL41.Contig21_All), _caffevol-CoA-O-methyltransferasesferase_ (CL11417.Contig1_All), _cinnamyl-alcohol dehydrogenase_ (CL5952.Contig4_All) were drastically up-regulated from 0 to 100 \(\upmu\)M MeJA treatment (Figures 5A and S8). The result showed that 10 \(\upmu\)M MeJA treatment can significantly induce the DEGs expression of phenylpropanol biosynthesis compared to 50 and 100 \(\upmu\)M MeJA in rosemary suspension cells. To reveal the potential key genetic factors in rosemary suspension cells under different concentrations of MeJA, we found a total of 35 DEGs were assi  
Figure 5: DEGs assigned to phenylpropanol and flavonoid biosynthesis pathway under MeJA treatments.