## 3 Results
### RNA-Seq Analysis of Rosemary Suspension Cells  
To study the effects of different concentrations of MeJA on rosemary suspension cells at a transcriptional level, four mRNA libraries were constructed and sequenced from the four concentrations of MeJA treatment (CK_(1,2,3), M10_(1,2,3), M50_(1,2,3) and M100_(1,2,3)). After removing the linker sequence, the RNA-Seq data of the twelve rose-mary suspension cells libraries produced 66,314,608 to 71,191,500 reads, respectively, due to differences in concentrations of MeJA. The values of Q20 were higher than 97% in all the samples, indicating the high reliability of the rosemary suspension cells transcriptome sequencing data (Tables S2-S4). In addition, unigenes were exposed to Nr, Nt, SwissPort, Pfam, KEGG, GO and KOG databases using BLAST analysis (E-value \(<\) 0.00001) (Table S5). The unigenes annotated in the Nr database were counted, the top five species were annotated: _Sesamtum indicum_ L. (65.02%), _Erythmenthe guttata_ L. (17.59%), _Doroceras hygrometricum_ L. (2.08%), _Salvia milliorrhiza_ L. (2.08%) and _Ipomoae nil_ L. (0.75%). The 17.59% and 2.08% of the total number of Nr annotations accounted for, respectively, 2.08% and 0.75% (Figure S1). The distribution of gene functions in GO was grouped into biological processes, cellular component and molecular function, cellular process (14,755 unigenes), cell (14,796 unigenes), binding (25,721 unigenes) and catalytic activity (23,776 unigenes) were dominant subcategories (Figure S2). Similarly, KOG functional classification showed that the uppermost classification was general function prediction only (15,177 unigenes) followed by signal transduction mechanisms (9078 genes). In addition, 1205 unigenes were annotated for secondary metabolites biosynthesis, transport and catabolism (Figure S3). At last, unigenes were also annotated against KEGG database for understanding advanced-level utilities and functions of the biological structure. Among 80,961 unigenes were annotated in 136 pathways, metabolism (102 pathways, 40,920 unigenes) was the most significant category, a substantial number of genes were related to carbohydrate metabolism (6277 genes) and amino acid metabolism (3835 gens) (Figure S4). Global Analysis of Gene Expression across the Four Distinct Samples under Different Concentrations of MeJA  
In our study, there were 107,512, 102,762, 107,366 and 107,646 expressed genes in CK, M10, M50 and M100 sample libraries. Among these, 103,386 expressed genes were present in all four sample libraries. However, only 572, 621, 531 and 571 genes were uniquely present in CK, M10, M50 and M100 sample libraries, respectively (Figure 2A), which suggested that distinct spatial transcriptional patterns were present in the sample libraries. In order to evaluate the differences in molecular response among four samples, gene expression was normalized to FPKM. After filtering with FPKM\(>\) 10, a total of 14,104 (13.11%), 13,880 (12.87%), 13,981 (12.97%) and 13,940 (12.95%) genes were expressed in CK, M10, M50 and M100, respectively (Table S6). The top 20 most enriched (FPKM) genes ranged from 682 to 3814, 781 to 3294, 663 to 3844 and 709 to 4294, respectively. The top 20 most expressed genes from the four libraries were shown as _defensin-like cystein-rich peptide_, _extracellular ribonuclease LE_, _PREDICTED: titin-like_, _pathogen-related protein STH-2_, _hypothetical protein SELMODRAFT_431225_, _aquaporin-like protein_, _partial, major pollen allergen Lol p 11-like and extensin-3_--highly expressed in CK, M10, M50 or M100 sample libraries (Table S7). To further understand the changes in the rosemary suspension cells transcriptome under different concentrations of MeJA, Poisson D was used to calculate the expression level of each gene.