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We performed an integrated analysis of the transcriptome and metabolome from purple (Pr) and normal cultivated varieties (CK) of  Dendrobium officinale  to gain insights into the regulatory networks associated with phenylpropanoid metabolism and to identify the key regulatory genes of pigmentation .  Metabolite and transcript profiling were conducted by ultra-performance liquid chromatography electrospray tandem mass spectrometry (UPLC-ESI-MS/MS) and RNA sequencing. Pr had more flavonoids in the stem than did CK. Metabolome analyses showed that 148 differential metabolites are involved in the biosynthesis of phenylpropanoids, amino acids, purines, and organic acids. Among them, the delphinidin and quercetin derivatives were significantly higher in Pr. A total of 4927 differentially expressed genes (DEGs) were significantly enriched ( p  ≤ 0.01) in 50 Gene Ontology (GO) terms. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed significantly enriched phenylpropanoid biosynthesis and phytohormone signal transduction in Pr versus CK. The expression levels of  flavanone 3-hydroxylase  ( F3H ) and  leucoanthocyanidin dioxygenase  ( LDOX ) affected the flux of dihydroflavonol, which led to a color change in Pr. Moreover, DEG enrichment and metabolite analyses reflected flavonoid accumulation in Pr related to brassinosteroid (BR) and auxin metabolism. The results of this study elucidate phenylpropanoid biosynthesis in  D. officinale .

Metabolomic and transcriptomic analyses reveal the regulation of pigmentation in the purple variety of Dendrobium officinale