Objective Differential gene expressions (DEGs) and metabolite syntheses in the stems and leaves of Dendrobium huoshanense were studied by transcriptome and metabolome analyses.

Method Morphology of the organs was observed under a scanning electron microscope (SEM), non-targeted and carbohydrate metabolomics analyzed using high-performance liquid chromatography-mass spectrometry, and DEGs and KEGG enrichment pathways identified by transcriptome sequencing.

Result Surfaces of the stems and both adaxial and abaxial leaf of D. huoshanense had a flaky, waxy structure with long-chain fatty acids dominated in the stems (61.5%) and long-chain branched fatty acids in the leaves (23.3%). Transcriptome sequences of the genes showed 2,330 to be upregulated and 4,016 downregulated in the stems, as compared to those in the leaves. The most significantly enriched KEGG pathways in the organs were associated with hormone signal transduction and plant-pathogen interaction. They were followed by flavonoids and monoterpenoids biosynthesis pathways. Among the non-targeted metabolites detected in the stems, 113 were benzenes and derivatives, 194 carboxylic acid derivatives, 139 fatty acyls, 147 organic oxides, and 198 terpenoid lipids in the stems; and those in the leaves, 129, 187, 134, 155, and 221, respectively. Flavonoid glycosides accounted for the highest proportion of 58.1% in the stems and 59.2% in the leaves; whereas sesquiterpenoids were relatively abundant in the stems at 27.43% and diterpenoids highest in the leaves at 44.95%. There were 20 types of carbohydrates, including sucrose (77.62 mg·g⁻¹), glucose (47.11 mg·g⁻¹), and D-fructose (7.40 mg·g⁻¹), found in the stems.

Conclusion The multi-omics analysis unveiled differentiate types and contents of secondary metabolites in the stems and leaves of D. huoshanense. Along with the enriched DEGs and associated metabolic pathways identified in this study, the metabolic mechanisms in and utilization of the different parts of the medicinal material could be better defined.