## 3 Results
### KEGG Enrichment and Mapman Analysis of DEGs in Rosemary Suspension Cells
Galactose metabolism, phenylpropanol biosynthesis, vitamin B6 metabolism, ascorbate and aldarate metabolism were enriched in the three comparisons among the top 20 pathways (Figure 4). This indicated that these pathways differed significantly under different MeJA concentrations treatments. Some pathways were enriched in the top 20 in two combinations, photosynthesis-antenna proteins, photosynthesis and RNA polymerase were enriched in the top 20 in CKvsM10 and CKvsM50 (Figure 4). This indicated that these pathways might play important roles in responding to 10 and 50 uM MeJA treatments. Glycosaminoglycan degradation and pentose and glucuronate interconversions were enriched in the top 20 in CKvsM10 and  
Figure 4: The top 20 KEGG pathways enriched by DEGs in in the comparisons. Red indicates significant enrichment and gray indicates no significant enrichment. CKvsM100 (Figure 4), suggesting that 10 and 100 uM MeJA were more effective for them. Benzoxazinoid biosynthesis, sesquiterpenoid and triterpenoid biosynthesis, plant hormone signal transduction and carotenoid biosynthesis were enriched in the top 20 in CKvsM50 and CKvsM100 (Figure 4), suggesting that 50 and 100 uM MeJA were more effective for these pathways. Some pathways were only enriched in the top 20 for one combination (Figure 4). MAPK signaling pathway-plant, indole alkaloid biosynthesis, ABC transporters, and phenylalanine, tyrosine and tryptophan biosynthesis were only enriched in the top 20 in CKvsM10. linoleic acid metabolism, zeatin biosynthesis, flavonoid biosynthesis, diterpenoid biosynthesis and ubiquinone and other terpenoid-quinone biosynthesis were only enriched in the top 20 in CKvsM50. Tryptophan metabolism, isoquinoline alkaloid biosynthesis, alpha-Linolenic acid metabolism, tyrosine metabolism and steroid biosynthesis were only enriched in the top 20 in CKvsM100, indicating that 50 and 100 uM MeJA were more effective than 10 uM MeJA for metabolites such as terpenoids and flavonoids. Mapman analysis of the DEGs was distributed in the cell wall, lipids, ascorbate and glutathione, sucrose and amino acid pathways (Figure S6A-C). More up-regulated DEGs were identified in the CKvsM100 comparison than the CKvsM10 and CKvsM50 comparisons in lipids, ascorbate and glutathione and amino acid pathways. More DEGs were identified in the CKvsM50 and CKvsM100 than the CKvsM100 comparison in the flavonoid metabolism pathway and more numbers of up-regulated DEGs were identified in the CKvsM50 and CKvsM100 comparisons. More DEGs were identified in the CKvsM10 and CKvsM100 than the CKvsM50 comparison in Non-MVA, MVA and phenylpropanoids pathways (Figure S6D-F). The above results indicate that 100 uM MeJA affected the metabolism including amino acids lipids, ascorbate, glutathione terpenoids and total flavonoids significantly more than 10 and 50 uM MeJA in rosemary suspension cells. GO and KEGG enrichment and Mapman analyses of the DEGs showed that MeJA affected the synthesis of rosemary suspension cells' metabolites via multiple pathways, including plant hormone signal transduction, reactive oxygen species (ROS) clearance, osmotic balance, phenylpropanoid biosynthesis and many other metabolism pathways that may play important regulatory roles. Differential Expression Analysis of Plant Hormone Signal Transduction Related Genes during Rosemary Suspension Cells under Different Concentrations of MeJA  
To reveal the potential key genetic factors in rosemary suspension cells under different concentrations of MeJA, we found a total of 16 DEGs were assigned to JA biosynthesis, including 1 _LOX25_, 2 _AOS_, 1 _AOC_, 2 _OPR_, 1 _OPCL1_, 7 _ACX_, 1 _MEP2_ and 1 _J-O-MT_. _LOX25_, _OPCL1_ and _ACX_ (Unigene8348_All, Unigene10587_All) were up-regulated from 0 to 100 uM MeJA treatments, _OPR_ (Unigene16468_All) and _ACX_ (Unigene3995_All, Unigene819_All) were down-regulated from 0 to 100 uM MeJA treatments. _AOS_ was down-regulated under 10 uM MeJA treatment but up-regulated under 100 uM MeJA treatment.