Flavonoid biosynthesis in four Dendrobium species based on transcriptome sequencing and metabolite analysis

Background Dendrobium is a genus of plants used as traditional Chinese herbal medicines, with high economic and medicinal value. Methods and results To reveal the mechanism of flavonoid biosynthesis in Dendrobium , the metabolites and transcriptomes of four Dendrobium species ( D. chrysotoxum , D. nobile , D. fimbriatum , and D. denneanum ) were analyzed comprehensively. Ultra-high-performance liquid chromatography-tandem mass spectrometry analysis revealed ten flavonoid compounds in Dendrobium . In total, 100,096 unigenes were obtained from the transcript database of the four Dendrobium species. Among the identified differentially expressed genes, 51 were associated with flavonoid biosynthesis, and 670 differentially expressed transcription factors were predicted, including 194 MYB, 87 bHLH, and 100 WRKY family transcription factors, respectively. Transcriptome analysis showed that the expression levels of structural genes such as chalcone synthase ( CHS ), cinnamate-4-hydroxylase ( C4H ), and flavonoid 3′-hydroxylase ( F3′H ) were lower in D. chrysotoxum , D. nobile , and D. fimbriatum than those in D. denneanum , which may be the main reason for the low flavonoid contents in D. chrysotoxum , D. nobile , and D. fimbriatum . Conclusions The expression level of structural genes corresponded to the accumulation level of flavonols in the different Dendrobium species. The results deepen the understanding of the molecular mechanism of flavonoid biosynthesis in Dendrobium and provide novel insights into the synthesis and accumulation of flavonoids in Dendrobium .