ORIGINAL RESEARCH article
Front. Plant Sci.
Sec. Plant Metabolism and Chemodiversity
Volume 16 - 2025 | doi: 10.3389/fpls.2025.1636028
This article is part of the Research TopicUnraveling the Metabolic Diversity of Phytochemical-Rich Plants: Integrative Metabolomics ApproachesView all articles
Integrated Metabolomic and Transcriptomic Analysis Elucidates Transcriptional Regulation of Flavonoid Biosynthesis in Differentially Pigmented Honeysuckle (Lonicera japonica) Varieties
Provisionally accepted
- 1College of Basic Medical Science, Ningxia Medical University Yinchuan, Yinchuan, China
- 2Guyuan Branch of Ningxia Academy of Agricultural and Forestry Sciences, Guyuan, China
- 3Institute of Forestry and Grassland Ecology, NingXia Academy of Agriculture and Forestry Sciences, Yinchuan, China
- 4Life College, Ningxia University, Yinchuan, China
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Honeysuckle (Lonicera japonica Thunb.) is a traditional medicinal plant prized for its bioactive flavonoids, which confer antiviral, anti-inflammatory, and antioxidant properties. Despite its pharmacological significance, the genetic and metabolic basis of flavonoid accumulation and flower color differentiation among cultivars remains poorly understood. Here, we compared two honeysuckle varieties-'Luyu No.1' (white-yellow flowers) and 'Honghua' (red-pink flowers)-during the 'Dabai period' (optimal harvest stage) using transcriptomics and metabolomics.RNA-seq identified 5,901 differentially expressed genes (DEGs), with pronounced enrichment in phenylpropanoid and flavonoid biosynthesis pathways. Key structural genes-PAL, CHS, F3H, FLS, DFR, and ANS-were upregulated in 'Honghua', correlating with its 2.32-fold higher total flavonoid content. Metabolomic profiling detected 399 flavonoids, including 228 differentially accumulated metabolites (DAMs), with 'Honghua' exhibiting elevated anthocyanidins (87.58-fold higher), flavanols (7.66-fold higher), and chalcones (6.17-fold higher). Critical metabolites such as quercetin-3-O-rhamnoside and luteolin-7-O-glucoside were significantly enriched in 'Honghua', linked to its red-pink pigmentation.Integrated analysis highlighted the role of transcription factors (MYB, bHLH, NAC) in modulating flavonoid pathways. Notably, TCP15 (bHLH) was down-regulated in 'Honghua', while F3'M and 3RT (anthocyanin-modifying enzymes) were up-regulated 22.12-and 3.03-fold, respectively, driving anthocyanin diversification. These findings elucidate how coordinated gene-metabolite networks govern flavonoid divergence, with 3RT and F3'M emerging as key determinants of flower color and medicinal quality.This study provides the first comprehensive framework for flavonoid biosynthesis in honeysuckle, offering genetic targets for breeding high-flavonoid cultivars with enhanced therapeutic potential.
Keywords: Lonicera japonica, Flavonoid biosynthesis, Transcriptomics, Metabolomics, Anthocyanins, MYB transcription factors
Received: 27 May 2025; Accepted: 20 Aug 2025.
Copyright: © 2025 Liao, Wu, Xie, He, Zhang, Liu, Li, Dai and Wang. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence:
Hua Liu, Institute of Forestry and Grassland Ecology, NingXia Academy of Agriculture and Forestry Sciences, Yinchuan, China
Ming Li, Institute of Forestry and Grassland Ecology, NingXia Academy of Agriculture and Forestry Sciences, Yinchuan, China
Lijuan Wang, College of Basic Medical Science, Ningxia Medical University Yinchuan, Yinchuan, China
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