## 3 Results
### Transcriptional Profiling
Statistical significance was calculated using GraphPad Prism 8 (Version 8.0.2, GraphPad Software, La Jolla, CA, USA). *_p_ < 0.05; **_p_ < 0.01. Figure 3: Heat map analysis of the overall gene expression profiles and Kyoto Encyclopedia of Genes and Genomes (KEGG) category distribution of the DEGs in the six expression subclusters composing the transcriptome of _D. officinal_ leaves under salt stress. (**A**) The hierarchical analyses of co-expression transcripts at different time points of salt stress. Blue indicates the downregulated and red indicates the upregulated expression of genes. Expression values were Z-scaled (log\({}_{2}\)(FPKM+1)). (**B**) Six subclusters of expression patterns and KEGG enrichment categories. Expression values were Z-scaled. The blue line represents the average expression value of the members at each time point. The degree of enrichment of categories in each cluster is shown in different colored boxes. Red represents the over-represented categories and blue represents the under-represented categories. KEGG category enrichment was computed using the Cluster package and \(q\) value package (\(q\) value \(<\) 0.05) in R.  
Transcription factors (TFs) are considered to be the most important regulators controlling gene expressions. A total of 31 _bHLH_s (10 upregulated and 21 downregulated), 29 _MYBs_ (8 upregulated and 21 downregulated), 17 _WRKYs_ (7 upregulated and 10 downregulated), 110 _RLK-Pelles_ (53 upregulated and 57 downregulated), 22 _NACs_ (11 upregulated and 11 downregulated), and 49 _AP2/ERFs_ (19 upregulated and 30 downregulated) were differentially expressed under the salt stress treatment compared with under the control treatment (Figure S1). These differently expressed TFs may be critical genes in responses to salt stress. Transcriptome data analysis showed that the expression level of _DobHLH_ (_gene9655_) was significantly downregulated under salt stress (Figure S2A). Putative protein DoTIFY10 As (gene3248 and gene3249 ) and DoTIFY10 Bs (gene20757, gene28238, and gene13335) that interact with protein DobHLH (gene9655) were identified by blasting in the STRING database (Figure S2B). The sequence of protein DobHLH (gene9655) was blasted in the Plant Transcription Factor Database ([[http://planttfdb.gao-lab.org/blast.php](http://planttfdb.gao-lab.org/blast.php)]([http://planttfdb.gao-lab.org/blast.php](http://planttfdb.gao-lab.org/blast.php)), accessed on 1 March 2021). It was found that DobHLH (gene9655) was highly homologous with _Arabidopsis thaliana_ MYC4 (AtMYC4) (Table S3). In addition, AtMYC4 interacts with some proteins in the JA ZIM-domain protein (JAZ), F-box protein CORONATINE INSENSITIVE1 (COI1), and TIFY transcription factor families (Figure S2C). Transcriptional expression profiles showed that the expression levels of some _DoTIFY10 As_ and _DoTIFY10 Bs_ were upregulated under salt stress (Figure S3). Therefore, it is speculated that DobHLH (gene9655) may also interact with some proteins in the JAZ, COI1, and TIFY transcription factor families in _D. officinal_. Furthermore, the expression level of _DoMYB_ (_gene6015_) was significantly upregulated under salt stress (Figure S4A). Thirteen proteins that interact with DoMYB (gene6015) were obtained in the STRING database (Figure S4B). It was found that DoMYB (gene6015) was most homologous with _A. thaliana_MYBTT2 (AtMYBTT2, Alias: AtMYB123) by blasting its protein sequence into the Plant Transcription Factor Database (Table S4 and Figure S5). In addition, AtMYBTT2 interacts with AtDFR and AtF3H proteins (Figure S4C). Therefore, it is speculated that DoMYB (_gene_6015_) may also interact with DFR and F3H proteins in _D. officinal_. Figure 4: The jasmonic acid (JA) biosynthetic pathway and related upregulated genes under salt treatment. (**A**) The JA biosynthetic pathway and its associated enzymes. (**B**) Heat map analysis of upregulated gene expression in the JA biosynthetic pathway under salt treatment.