A Comparison of the Flavonoid Biosynthesis Mechanisms of <i>Dendrobium</i> Species by Analyzing the Transcriptome and Metabolome

Dendrobium huoshanense, Dendrobium officinale, and Dendrobium moniliforme, as precious Chinese medicinal materials, have a variety of medicinal properties. Flavonoids are important medicinal components of Dendrobium, but their accumulation rules and biosynthesis mechanisms remain unclear. To explore the similarities and differences of flavonoid accumulation and biosynthesis in these three Dendrobium species, we performed flavonoid content determination, widely-targeted metabolomics and transcriptome sequencing on 1–4 years old Dendrobium species. The results showed that in different growth years, D. huoshanense stems had the highest flavonoid content in the second year of growth, while D. officinale and D. moniliforme stems had the highest flavonoid content in the third year of growth. A total of 644 differentially accumulated metabolites (DAMs) and 10,426 differentially expressed genes (DEGs) were identified by metabolomic and transcriptomic analysis. It was found that DAMs and DEGs were not only enriched in the general pathway of “flavonoid biosynthesis”, but also in multiple sub-pathways such as “Flavone biosynthesis”, and “Flavonol biosynthesis” and “Isoflavonoid biosynthesis”. According to a combined transcriptome and metabolome analysis, the expression levels of the F3′H gene (LOC110096779) and two F3′5′H genes (LOC110101765 and LOC110103762) may be the main genes responsible for the differences in flavonoid accumulation. As a result of this study, we have not only determined the optimal harvesting period for three Dendrobium plants, but also identified the key genes involved in flavonoid biosynthesis and provided a basis for further study of the molecular mechanism of flavonoid synthesis