## 5 Conclusions  
We carried out transcriptome and metabolite profiling to illuminate the response mechanisms of _D. officinal_ leaves under salt stress. The DEGs related to the biosynthesis pathways of JA and flavonoids in _D. officinal_ leaves have been identified. The results demonstrated that salt stress could trigger JA biosynthesis, and JA, which as a signal molecule, further promotes flavonoid biosynthesis. Therefore, for _D. officinal_ plants, the application of exogenous MeJA may increase the content of secondary metabolites such as flavonoids in leaves. In addition, salt stress also increased the contents of other compounds, such as sugars and alkaloids, in _D. officinal_ leaves. The accumulation of these compounds, which have strong health benefits, may play an imperative role in how _D. officinal_ plants adapt to salt stress. These results could help to illustrate physiological response and molecular mechanisms in an important orchid plant _D. officinal_ under salinity stress and help to understand the relationship between quality and yield. **Supplementary Materials:** The following are available online at [[https://www.mdpi.com/article/10.3390/biom11050736/s1](https://www.mdpi.com/article/10.3390/biom11050736/s1)]([https://www.mdpi.com/article/10.3390/biom11050736/s1](https://www.mdpi.com/article/10.3390/biom11050736/s1)), Figure S1: Number of differentially expressed transcription factors (TFs) between salt stress and control treatments. (**A**) Number of both up- and downregulated TFs. (**B**) Number of upregulated TFs. (**C**) Number of downregulated TFs, Figure S2: The expression profile of bHLH transcription factor family genes and PPI networks. (**A**) Heat map analysis of gene expressions under salt stress. (**B**) The predicted PPI of DEGs obtained from the protein-protein interaction in the STRING database. (**C**) PPI networks of _A. thaliana_ genes homologous to _DobHLH_ (_gene9655_), Figure S3: The expression profile of TIF transcription factor family genes at different time points under salt stress, Figure S4: The expression profile of MYB transcription factor family genes and PPI networks. (**A**) Heat map analysis of gene expressions under salt stress. (**B**) The predicted PPI of DEGs obtained from the protein-protein interaction in the STRING database. (**C**) PPI networks of _A. thaliana_ genes homologous to _DoMYB_ (_gene6015_), Figure S5: Neighbor-joining phylogenetic tree showing the relatedness of the amino acid sequences of the _D. officinal_ MYB-related protein (accession number: XP 020672817.1) and 122 MYB-related proteins from _A. thaliana_. The MYB-related protein from _D. officinal_ is indicated with a red triangle. 'At' is an abbreviation for _A. thaliana_. The neighbor-joining phylogenetic tree was constructed using the MEGA 7 program with a bootstrap analysis of 1000 replicates. The accession numbers and amino acid sequences of the MYB-related protein from _D. officinal_ and 122 MYB-related proteins from _A. thaliana_ are shown in Table S6, Figure S6: PCA score plots (**A**), types (**B**), and KEGG pathway annotations of metabolites in leaves (**C**). 'Total' refers to the total types of identified metabolites. 'Up' and 'Down' refer the types of metabolites whose content is significantly increased and decreased, respectively, Figure S7: Putative simplified model of JA signaling in the biosynthesis of flavonoids. (**A**) JAZ and DobHLH (gene9655) interact to inhibit the response of JA under normal conditions. (**B**) Salt stress could trigger JA-Ile biosynthesis.