Transcriptomic and Metabolomic Analyses Reveal Differences in Flavonoid Pathway Gene Expression Profiles between Two Dendrobium Varieties during Vernalization

Abstract

Dendrobium (Orchidaceae, Epidendoideae) plants have flowers with a wide variety of colors that persist for a long period throughout the year. The yellow coloration of Dendrobium flowers is mainly determined by the flavonol pathway and the flavone pathway, but the relevant biosynthesis mechanisms during vernalization remain unclear. To explore the similarities and differences in flavonoid biosynthesis in different tissues during vernalization, we selected two species of Dendrobium for a flower color study: Dendrobium capillipes Rchb (which has yellow flowers) and Dendrobium nobile Lindl (which has white flowers). We collected a total of 36 samples from six tissue types and both Dendrobium species during vernalization and subjected the samples to metabolic profiling and transcriptome sequencing. A total of 31,504 differentially expressed genes (DEGs) were identified between different tissues of the two Dendrobium species by transcriptomic analysis. However, many differentially accumulated metabolites (DAMs) and DEGs were enriched not only in the general pathway of “flavonoid biosynthesis” but also in multiple subpathways of “flavone and flavonol biosynthesis”. According to a combined transcriptome and metabolome analysis, Putrescine hydroxycinnamoyl transferase 1 (LOC110093422) may be the main gene responsible for the differences in flavonoid accumulation during vernalization, which is closely associated with yellow flowers. Taken together, the results of our study preliminarily revealed the metabolites responsible for and the key genes regulating flavonoid biosynthesis during vernalization. These results provide a basis for the further study of the molecular mechanism of flavonoid synthesis during vernalization.

Combined transcriptome and widely targeted metabolome analysis reveals the potential mechanism of HupA biosynthesis and antioxidant activity in Huperzia serrata

“…Additionally, we discovered that PrAO and AST are also essential genes in this pathway in H. serrata . Furthermore, it was found that p-Coumaroyl-CoA, caffeoyl quinic acid, CHI , and CHS were identified as key metabolites and key genes in the antioxidant pathway, which aligns with previous reports ( Liu et al., 2022 ; Shu et al., 2023 ). Moreover, this study revealed that p-Coumaroyl quinic acid, 4-Coumaroylshikimate, 2,3-Dihydrofisetin, HCT , and CYP89A are newly discovered crucial metabolites and crucial genes.…”

Comparative Transcriptome Analysis and Expression of Genes Associated with Polysaccharide Biosynthesis in Dendrobium officinale Diploid and Tetraploid Plants

“…However, the differentiation in molecular mechanisms controlling the polysaccharide content between diploid and tetraploid D. officinale has remained unknown. A few studies have conducted transcriptome analyses for D. officinale considering different growth stages (juvenile to adult) [41], different plant parts (leaves, stems and roots) [43], flowers [57], and 2-year-old stems [58], and there have been studies on other Dendrobium species, such as D. huoshanense [57,59,60], D. catenatum [61], and D. moniliforme [62]. Therefore, this study has investigated transcriptomic profiles and some key genes related to polysaccharide biosynthesis tetraploid D. officinale.…”

“…These pathways are related to carbohydrate metabolism. The up-regulated DEGs in the BP vs. AP comparison for the top 20 KEGG pathways were significantly enriched in the spliceosome (121), mRNA surveillance pathway (86), glycolysis/gluconeogenesis (81), viral carcinogenesis (78), ribosome biogenesis in eukaryotes (70), phagosome and herpes simplex infection (57), and galactose metabolism (51) (Figure S4a). The down-regulated DEGs in the BP vs. AP comparison were significantly enriched in ribosome (312), biosynthesis of amino acids (218), protein processing in the endoplasmic reticulum (203), RNA transport (178), ribosome biogenesis in eukaryotes (115), and phagosome (82).…”

Metabolic and Transcriptomic Profile Revealing the Differential Accumulating Mechanism in Different Parts of Dendrobium nobile

“…Transcriptomic and metabolic analyses elucidated that some genes played vital roles in the transition from carbohydrate to alkaloid synthesis in the stems of D. nobile, such as DnAROG, DnPYK, DnDXS, DnACEE, and DnHMGCR [12]. Combined transcriptome and metabolome analysis revealed that DnPHT1 was one of the key genes regulating flavonoid biosynthesis in D. nobile [13]. Transcriptome analysis revealed that some genes like DnPMR6, DnPECS-2.1, DnSS1, and DnGLU3 led to an increase in the biosynthesis of polysaccharides in D. nobile [9].…”