the stem of Dendrobium huoshanense c.Z. tang and S.J. cheng was widely used as a medicinal herb in health care products due to its broad pharmacological activities. However, the molecular regulation mechanism of stem development and biosynthetic pathways of important bioactive substances are still unclear in D. huoshanense. in this study, the bioactive compounds in leaves, stems and roots, and the identification of candidate genes involved in stem formation and biosynthesis of active compounds via transcriptome sequence were analyzed. The accumulation of total polysaccharides and flavonoids were varied significantly in different tissues. A comparative transcriptomic analysis revealed several differentially expressed genes (DEGs) involved in polysaccharides biosynthesis (103 genes), including fructose and mannose related genes (29 genes) and glycosyltransferase genes (74 genes), and flavonoids biosynthesis (15 genes). Some candidate genes that participated in photoperiod regulation (27 genes), starch and sucrose metabolism (46 genes), and hormone-induced activation of signaling pathways (38 genes) may be involved in stem formation. In sum, this study provides a foundation for investigating the molecular processes in the biosynthesis of active compounds and stem development. the transcriptome data presented here provides an important resource for the future studies of the molecular genetics and functional genomics in D. huoshanense and optimized control of the active compounds produced by D. huoshanense.Dendrobium huoshanense C.Z. Tang and S.J. Cheng is an edible and medicinal plant, and has been utilized as a tonic in Traditional Chinese Medicine for centuries 1 . Specifically, it is used for boosting immunity, slowing aging, and possesses anti-tumor properties 2,3 . At present, increased demands and over-exploration caused reduced yield of wild resource and the damage of D. huoshanense habitats. Although artificial cultivation is an efficient way to protect natural resources and develop a sustainable medicinal supply, it was still faced an important issue to ensure and improve the quality and yield of D. huoshanense under artificial conditions. Understanding the regulation mechanism of quality and production of D. huoshanense has huge commercial and health value.At present, several ingredients from D. huoshanense have been identified as therapeutic active components, such as polysaccharides 4,5 , flavonoids 6,7 , alkaloids 8,9 . Modern pharmacological researches have confirmed that polysaccharides can activate immune cells, modulate the immune responses in the intestines, spleen, and liver, and inhibit cell proliferation in tumors [10][11][12][13] . Alkaloids possessed the functions of anti-inflammatory, anti-diabetic effect and anticancer activity 14,15 . Flavonoids also possesses biological functions including anti-oxidant, anti-cancer, anti-aging, cardiovascular protection, and building of immunity [16][17][18][19] . The key genes associated with polysaccharides and alkaloids biosynthesis have been identified,...

Background Perilla frutescens (L.) Britt is a medicinal and edible plant widely cultivated in Asia. Terpenoids, flavonoids and phenolic acids are the primary source of medicinal ingredients. Glandular trichomes with multicellular structures are known as biochemical cell factories which synthesized specialized metabolites. However, there is currently limited information regarding the site and mechanism of biosynthesis of these constituents in P. frutescens. Herein, we studied morphological features of glandular trichomes, metabolic profiling and transcriptomes through different tissues. Results Observation of light microscopy and scanning electron microscopy indicated the presence of three distinct glandular trichome types based on their morphological features: peltate, capitate, and digitiform glandular trichomes. The oil of peltate glandular trichomes, collected by custom-made micropipettes and analyzed by LC–MS and GC–MS, contained perillaketone, isoegomaketone, and egomaketone as the major constituents which are consistent with the components of leaves. Metabolomics and transcriptomics were applied to explore the bioactive constituent biosynthesis in the leaves, stem, and root of P. frutescens. Transcriptome sequencing profiles revealed differential regulation of genes related to terpenoids, flavonoids, and phenylpropanoid biosynthesis, respectively with most genes expressed highly in leaves. The genes affecting the development of trichomes were preliminarily predicted and discussed. Conclusions The current study established the morphological and chemical characteristics of glandular trichome types of P. frutescens implying the bioactive constituents were mainly synthesized in peltate glandular trichomes. The genes related to bioactive constituents biosynthesis were explored via transcriptomes, which provided the basis for unraveling the biosynthesis of bioactive constituents in this popular medicinal plant.

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Ampelopsis megalophylla is an important species used in Chinese folk medicine. Flavonoids, the most important active components of plants, greatly determine the quality of A. megalophylla. However, biosynthesis of flavonoids at the molecular and genetic levels in A. megalophylla is not well understood. In this study, we performed chemical analysis and transcriptome analysis of A. megalophylla in different seasons (i.e., May, August, and October). Accumulation of flavonoids was higher in May than in the other two months. Genes involved in the flavonoid biosynthesis pathway, such as chalcone synthase, anthocyanidin synthase, flavanone 3-hydroxylase, flavonoid-3′,5′-hydroxylase, caffeoyl-CoA O-methyltransferase, dihydroflavonol 4-reductase, 4-coumarate-CoA ligase, phenylalanine ammonia-lyase, cinnamate 4-hydroxylase, flavonoid 3′-monooxygenase, shikimate O-hydroxycinnamoyltransferase, and leucoanthocyanidin reductase, were identified based on transcriptome data. Fifty ATP binding cassette (ABC) transporter, nine SNARE, forty-nine GST, and eighty-four glycosyltransferases unigenes related to flavonoid transport and biomodification were also found. Moreover, seventy-eight cytochrome P450s and multiple transcription factors (five MYB, two bHLH, and three WD40 family genes) may be associated with the regulation of the flavonoid biosynthesis process. These results provide insights into the molecular processes of flavonoid biosynthesis in A. megalophylla and offer a significant resource for the application of genetic engineering in developing varieties with improved quality.