Integration of Transcriptome and Metabolome Provides New Insights to Flavonoids Biosynthesis in Dendrobium huoshanense

Abstract

Dendrobium huoshanense is both a traditional herbal medicine and a plant of high ornamental and medicinal value. We used transcriptomics and metabolomics to investigate the effects of growth year on the secondary metabolites of D. huoshanense stems obtained from four different years of cultivation. In this study, a total of 428 differentially accumulated metabolites (DAMs) and 1802 differentially expressed genes (DEGs) were identified. The KEGG enrichment analysis of DEGs and DAMs revealed significant differences in “Flavonoid biosynthesis”, “Phenylpropanoid biosynthesis” and “Flavone and flavonol biosynthesis”. We summarize the biosynthesis pathway of flavonoids in D. huoshanense, providing new insights into the biosynthesis and regulation mechanisms of flavonoids in D. huoshanense. Additionally, we identified two candidate genes, FLS (LOC110107557) and F3’H (LOC110095936), which are highly involved in flavonoid biosynthesis pathway, by WGCNA analysis. The aim of this study is to investigate the effects of growth year on secondarily metabolites in the plant and provide a theoretical basis for determining a reasonable harvesting period for D. huoshanense.

Selection of Suitable Reference Genes for Gene Expression Normalization Studies in Dendrobium huoshanense

“…Our research group on D. huoshanense has carried out a series of studies on the field resource protection, tissue culture and cultivation, chemical component separation and identification, bioactivity analysis and action mechanism, and new drug and product development [ 3 , 5 , 10 , 39 , 50 , 51 , 52 , 53 ], and also completed its whole genome sequencing [ 54 ]. In addition, the transcriptome sequencing of D. huoshanense had been reported several times in other research groups [ 13 , 14 , 15 , 16 , 17 ]. Since the main active components of similar plants have been gradually known, many studies also mainly focused on exploring and understanding the biological control [ 55 ] and biosynthetic pathways of polysaccharides, alkaloids and flavonoids, etc.…”

“…Since the main active components of similar plants have been gradually known, many studies also mainly focused on exploring and understanding the biological control [ 55 ] and biosynthetic pathways of polysaccharides, alkaloids and flavonoids, etc. [ 13 , 14 , 15 , 16 , 17 ].…”

“…However, the research on the gene expression of D. huoshanense is still not deep enough. Some key genes involved in the biosynthetic pathways of important components are unclear or remain theorized [ 13 , 14 , 15 , 16 , 17 ]. Even though some studies have carried out quantitative research on gene expression, the use of internal reference genes is usually selected by experience.…”

“…In recent years, plenty of studies have carried out gene and protein research on the biosynthetic pathway of D. huoshanense [ 13 , 14 , 15 , 16 , 17 , 20 , 21 ]. With the development of next-generation sequencing (NGS) technology, it has become simpler and faster to analyze the distribution of mRNA and their expression levels in the biosynthetic pathway of this plant [ 22 ].…”

“…The research on the biosynthetic pathway mechanisms of the polysaccharides, alkaloids, and flavonoids of D. huoshanense is the main concern of researchers in this field. Although previous studies have described some candidate genes related to D. huoshanense [ 13 , 14 , 15 , 16 , 17 , 39 ], it is still necessary to find appropriate reference genes for further enhancing the detection of different gene expression levels of D. huoshanense under different experimental conditions by using qPCR.…”