Objective  Pathway and genes related to the flavonoid synthesis in Dendrobium officinale were analyzed for studying on the metabolic regulation and medicinal applications of flavonoids.

  Method  Transcriptomes of the stems and leaves of D. officinale plants at two growth stages were determined by means of Illumina HiSeq 4000 high-throughput sequencing. The assembled unigenes were used for the functional annotation and genetic analysis of the flavonoid biosynthetic pathway.

  Result  There were 48 unigenes involving 14 enzymes found to be associated with the flavonoid metabolism. Among them, the 5 CHS-related unigenes showed a CHS-like conserved domain, highly conserved amino acid residues (Cys-His-Asn) at the active site, and mutated amino acid residues at the malonyl-CoA and product binding sites; and, the CHI (Unigene0013781) was identified as a Type I chalcone isomerase, isomerizing 6'-hydroxychalone to 5-hydroxyflavanone. The expressions of CHS (Unigene0008250), CHI (Unigene0013781) and F3H were higher than those of CHS (Unigene 0012884) and C3′H in the stems and leaves of the plants at both growth stages.

  Conclusion  Forty-eight unigenes involving 14 enzymes associated with the flavonoid metabolism in D. officinale plants were identified by the transcriptome analysis. Of the 5 CHS-related unigenes, two encoded chalcone synthase, and 3 bibenzyl synthase, while the CHI (Unigene0013781) a Type I chalcone isomerase.