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Integrative multi-omics, HPLC fingerprinting and machine learning reveal distinct differences among three Dendrobium species from the Dabie Mountains

ABSTRACT: Dendrobium species are widely used in traditional Chinese medicine owing to their medicinal and nutritional value, yet the phytochemical diversity and molecular mechanisms underlying theirbioactivities remain poorly understood. To elucidate these traits, we performed an integrative multi-omics study combining metabolomics and transcriptomics on three species, D. huoshanense, D. officinale, and D. moniliforme from the Dabie Mountains in Central China, with emphasis on flavonoid metabolism, particularly apigenin derivatives. Among 470 shared metabolites, quantitative profiling revealed distinct accumulation patterns between stems and leaves. Transcriptomic analysis uncovered species- and tissue-specific regulatory networks governing flavonoid biosynthesis. Complementary HPLC-DAD fingerprinting of stems, leaves, roots, and flowers was established and rigorously validated, with 18 common peaks annotated. VIP analysis identified tissue-specific chemical markers for quality assessment. Apigenin-6-C-α-L-arabinoside-8-C-β-D-xyloside and apigenin-6-C-α-L-rhamnosyl-(12)-β-D- glucoside-8-C-α-L-arabinoside were predominant in D. huoshanense stems, while flowers accumulated high levels of flavonoids such as rutin and vicenin-1 and displayed superior anti-inflammatory activity. Comprehensive nutritional profiling quantified total carbohydrates, polysaccharides, monosaccharides, fatty acids, amino acids, minerals, and vitamins across plant organs. Machine learning integration of multi-omics data delineated key molecular signatures distinguishing the three Dendrobium species from the Dabie Mountains. Together, this work provides a multidimensional resource that advances the biochemical understanding of Dendrobium, supports species and tissue discrimination, and informs quality control and utilization of both medicinal and edible plant parts.

INSTRUMENT(S): Liquid Chromatography MS - positive - hilic, Liquid Chromatography MS - negative - hilic

PROVIDER: MTBLS14876 | MetaboLights | 2026-06-28

REPOSITORIES: MetaboLights

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			Action	DRS
	a_MTBLS14876_LC-MS_negative_hilic.txt	Txt
	a_MTBLS14876_LC-MS_positive_hilic.txt	Txt
	i_Investigation.txt	Txt
	m_MTBLS14876_LC-MS_negative_hilic_v2_maf.tsv	Tabular
	m_MTBLS14876_LC-MS_positive_hilic_v2_maf.tsv	Tabular

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Project description:<p>Hemerocallis citrina Baroni is a traditional medical and edible plant with various health benefits. Currently, many phytochemical analyses have been performed and various biological constituents have been extracted from H. citrina. Flavonoid compounds are a kind of important bioactive components. However, the comparison of flavonoid compounds and antioxidant potentials of different tissues of H. citrina is not clear. In this study, we identified flavonoid metabolites and investigated antioxidant activities of four tissues including roots, stems, leaves and flowers of H. citrina. A total of 364 flavonoid metabolites were identified by UPLC-MS/MS based metabolomics, and the four tissues showed dramatic differences at flavonoid metabolic level. Compared to H. citrina roots, 185, 234 and 119 flavonoid metabolites accounted for upregulated DFMs in stems, leaves and flowers, respectively. Compared to stems, 168 and 29 flavonoid metabolites accounted for upregulated DFMs in leaves and flowers, respectively. Compared to leaves, only 29 flavonoid metabolites accounted for upregulated DFMs in flowers. A number of 35 common flavonoid metabolites were observed among six comparison groups, and each comparison group had its unique differential metabolites. The most abundant flavonoid metabolites in the four tissues are flavonols and flavones, followed by flavanones, chalcones, flavanols, flavanonols, anthocyanidins, tannin and proanthocyanidins. The dominant DFMs in roots are 6,7,8-Tetrahydroxy-5-methoxyflavone, 7,8,3',4'-tetrahydroxyflavone, 1-Hydroxy-2,3,8-trimethoxyxanthone, Farrerol-7-O-glucoside, 3',7-dihydroxy-4'-methoxyflavone, 3,3'-O-Dimethylellagic Acid, 5-Hydroxy-6,7-dimethoxyflavone, Nepetin (5,7,3',4'-Tetrahydroxy-6-methoxyflavone), (2s)-4,8,10-trihydroxy-2-methoxy-1h,2h-furo[3,2-a]xanthen-11-one. The dominant DFMs in stems are Isorhamnetin-3-O-(6''-malonyl)glucoside-7-O-rhamnoside, 7-Benzyloxy-5-hydroxy-3',4'-methylenedioxyflavonoid, 3-Hydroxyphloretin-4'-O-glucoside. The dominant DFMs in leaves are Chrysoeriol-7-O-glucoside, Epicatechin glucoside, Kaempferol-3-O-rhamnoside (Afzelin)(Kaempferin)*, Azaleatin (5-O-Methylquercetin), Chrysoeriol-5-O-glucoside, Nepetin-7-O-glucoside(Nepitrin), 3,5,7,2'-Tetrahydroxyflavone; Datiscetin, Procyanidin B2*, Procyanidin B3*, Procyanidin B1, Isorhamnetin-3-O-(6''-acetylglucoside). The dominant DFMs in flowers are kaempferol-3-p-coumaroyldiglucoside, Delphinidin-3-O-sophoroside-5-O-glucoside, Limocitrin-3-O-sophoroside, Kaempferol-3-O-rutinoside(Nicotiflorin), Luteolin-7-O-(6''-malonyl)glucoside-5-O-rhamnoside. The total flavonoid contents (TFC) and antioxidant activities of different tissues were in the order of leaves>stems>flowers>roots. The positive correlation was shown between TFC and the antioxidant activity values obtained from DPPH, ABTS and FRAP assays. There was significant difference in flavonoid metabolites among different tissues of H. citrina. Leaves had higher metabolites and antioxidant capacity than other tissues. This study promoted comprehensive resource utilization of H. citrina and provided biological and chemical evidence for the different uses of various plant tissues.</p>

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Integrative multi-omics, HPLC fingerprinting and machine learning reveal distinct differences among three Dendrobium species from the Dabie Mountains

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