Integrated metabolomic and transcriptomic analysis of Camellia sinensis var. pubilimba 'Rucheng Baimaocha' reveals distinct flavonoid and strictinin biosynthesis.
This study revealed a unique pattern of bioactive compound accumulation in RCBMC and provides valuable germplasm resources and genetic targets for breeding tea cultivars with enhanced functional components.
Abstract
Background
'Rucheng Baimaocha' (RCBMC) is a traditional tea landrace found in Hunan Province, China. Its morphological characteristics differ substantially from those of the other cultivars, featuring larger mature leaves with thicker cuticle layers. Both young buds and leaf undersides are densely covered in silvery-white trichomes, indicating that RCBMC has a distinct metabolite composition compared to other cultivars. To elucidate the metabolic profile differences and their underlying molecular mechanisms, we conducted an integrated metabolomic and transcriptomic analysis of RCBMC and representative cultivars.
Results
Metabolomics revealed that RCBMC accumulated higher levels of non-epicatechins, such as catechin, catechin gallate, and gallocatechin gallate, and the ellagitannin strictinin, whereas flavonoid glycosides were significantly lower. Transcriptomics identified 11,775 differentially expressed genes with key shifts in the flavonoid pathway: upregulated LAR and downregulated ANS gene expression collectively redirected metabolic flux toward non-epicatechin synthesis. The downregulation of multiple UGT genes was correlated with reduced flavonoid glycoside levels. Weighted gene co-expression network analysis further identified transcription factors strongly associated with metabolite accumulation. Quantitative analysis of 607 medium- and small-leaf tea germplasms indicated that strictinin content was genetically influenced and seasonally regulated, with RCBMC exhibiting notably high levels. Correlation analysis identified candidate genes from the SCPL, CXE, and LAC families that are potentially involved in strictinin biosynthesis.
Conclusions
This study revealed a unique pattern of bioactive compound accumulation in RCBMC and provides valuable germplasm resources and genetic targets for breeding tea cultivars with enhanced functional components.
Sour jujube (Ziziphus jujuba var. spinosa) is a valuable medicinal and edible fruit owing to its health-promoting properties. Methoxylated flavonoids enhance their value by improving stability and bioavailability. However, the cellular basis of their biosynthesis remains unclear. We constructed a single-nucleus transcriptomic atlas of sour jujube fruit. Parenchyma cells were identified as the primary sites for flavonoid biosynthesis and their O-methylation, characterized by high expression of phenylpropanoid pathway genes and O-methyltransferases (OMTs). Among the 48 identified OMTs, four (ZjOMT1–4) exhibited high expression, phylogenetically clustered with known functional OMTs, and localized to the cytoplasm; they were further characterized by enzyme activity assays. Notably, ZjOMT1 demonstrates moderate substrate promiscuity, catalyzing the methylation of various substrates, including quercetin, quercitrin, and rutin. Our findings reveal the cellular architecture of flavonoid metabolism in sour jujube fruit, providing genetic resources for breeding varieties with enhanced flavonoid profiles to develop functional foods and nutraceuticals.
Guo-Long Li, Hong-Hong Jiao, Wan-Li Zhao et al.· Journal of Agricultural and...· 0 citations
Simple Summary Evodia rutaecarpa (Juss.) Benth. is a classic traditional Chinese medicinal plant with significant pharmacological activities, and its dried fruits are the officially recognized medicinal part. While most existing research focuses on the fruit, the metabolic and transcriptional characteristics of non-medicinal tissues (roots, stems, leaves, and flowers) remain underexplored, which hinders the full utilization of E. rutaecarpa plant resources. To address this gap, we conducted an integrated analysis combining widely targeted metabolomics and transcriptomics to profile the metabolic and transcriptional landscapes across four tissues of E. rutaecarpa. Our results revealed pronounced tissue-specific secondary metabolic differentiation: roots specifically accumulated quinolone alkaloids and flavonoid glycosides, whereas leaves, stems, and flowers preferentially accumulated bioactive indole alkaloids (evodiamine and rutaecarpine). Notably, leaves and flowers exhibited particularly high accumulation levels of these active alkaloids, indicating their potential as alternative sources for industrial and pharmaceutical production. We further identified key candidate structural genes and regulatory gene modules associated with indole alkaloid biosynthesis. Collectively, our findings provide a systematic foundation for the comprehensive utilization of E. rutaecarpa resources and lay a solid groundwork for future metabolic engineering of bioactive indole alkaloids.
Wei-Wei Zhao, Ji-Hua Guo, Tai-Hang Wang et al.· Biology· 0 citations
Paeonia lactiflora Pall. (Chinese peony), a perennial plant indigenous to northeastern China, exhibits extensive flower-color variation, but the metabolite-gene relationships underlying anthocyanin accumulation remain incompletely understood. We integrated metabolomic and transcriptomic of petals from three cultivars with pink (cv. ‘Exclusive Memory’, PF), pale pink (cv. ‘Salad’, PPF), and white (cv. ‘Duchess’, WF) flowers. Metabolomic profiling detected 689 metabolites, including 169 flavonoids and six anthocyanins. Pairwise comparisons identified 153, 199, and 137 differentially accumulated metabolites in PF vs. PPF, PF vs. WF, and PPF vs. WF, respectively, with 27 metabolites shared among the three comparisons. The total anthocyanin signal in PF petals was 3.25-fold that in PPF petals and 60.37-fold that in WF petals. By contrast, the abundance of the individual compound cyanidin-3,5-O-diglucoside (cyanin) was 76.85-fold higher in PF than in WF and 23.10-fold higher in PPF than in WF, these values therefore describe compound-specific rather than total-anthocyanin differences. RNA-seq identified 6,777, 8,030, and 6,794 differentially expressed genes in the three pairwise comparisons, including 779 shared genes. Correlation analysis prioritized 21 flavonoid-pathway structural genes and 53 candidate transcription factors associated with anthocyanin abundance. Weighted gene co-expression network analysis identified a turquoise module positively associated with anthocyanins and a DFR-centered subnetwork containing 24 candidate transcription factors, including MYB and bHLH genes. qRT-PCR of 12 selected genes reproduced the RNA-seq expression trends. These results elucidate the metabolic basis of peony petal coloration and identify candidate regulatory networks and key genes potentially involved in anthocyanin biosynthesis, providing a foundation for future functional validation.
Yang Cao, Pin Lv, Yong-Chuan Guo et al.· Frontiers in Plant Science· 0 citations
These findings collectively support flavanone 3-hydroxylase (F3H) as a candidate regulatory node governing organ-specific flavonoid partitioning in Rhododendron yedoense var.
The flavor variation among different tea plant cultivars significantly influences their economic value. ‘Huangjinya’ (HJY), a typical light-sensitive etiolated tea cultivar, is prized for its fresh and mellow taste with low bitterness and astringency, and commands a high market value, serving as excellent germplasm for breeding superior-flavor tea varieties. Previous studies have largely focused on the mechanisms underlying fresh and umami tastes, whereas the regulatory mechanisms underlying bitterness and astringency remain poorly understood. In this study, two tea plant (Camellia sinensis (L.) O. Kuntze) cultivars with distinct bitterness and astringency phenotypes, namely ‘Fuxuan 9’ (FX) and HJY, were used to investigate the formation mechanism of reduced bitterness and astringency through integrated metabolomic and transcriptomic analyses. Metabolomic profiling identified 601 differentially accumulated metabolites between the two cultivars, which were significantly enriched in the flavonoid biosynthesis pathway. Notably, although the total flavonoid content was higher in HJY, the accumulation of non-esterified catechins (C, EC, EGC), which are key contributors to bitterness, was significantly lower than in FX. By contrast, the levels of esterified catechins (EGCG, GCG) showed no marked differences between cultivars. This distinct accumulation pattern provides a metabolic basis potentially associated with the reduced bitterness and astringency in HJY. Transcriptomic analysis revealed that the catechin biosynthetic gene CsLAR was significantly down-regulated in HJY, consistent with the reduced accumulation of non-esterified catechins. Promoter cloning and functional validation confirmed that the CsLAR promoters in both cultivars were active, which differed by only one regulatory element. Under shading treatment, CsLAR expression in HJY was more sensitive to light and decreased more markedly, suggesting that the expression of CsLAR may be regulated by transcription factors. Furthermore, 385 differentially expressed transcription factors were identified, with predicted binding sites in the CsLAR promoter region, implying their potential involvement in modulating catechin accumulation through modulation of CsLAR expression. Together, these multi-omics findings reveal molecular features potentially contributing to the low bitterness and astringency of HJY, providing a theoretical basis and candidate regulators for breeding tea cultivars with improved flavor profiles.
Ling-Hui Wang, Quan Xu, Miao Xu et al.· Plants· 0 citations
Mirabilis himalaica is a Tibetan medicinal plant whose tuberous root is its principal medicinal organ. To characterise molecular and metabolic differences associated with root enlargement, we integrated untargeted metabolomic and transcriptomic analyses of enlarged and non-enlarged roots. We identified 1465 metabolites, including 336 differentially accumulated metabolites, and 4058 differentially expressed genes. Flavonoids and phenolic acids were predominantly less abundant in enlarged roots, whereas several alkaloids showed higher relative abundance. Three gibberellin-related metabolites were lower in enlarged roots, while 1-Aminocyclopropanecarboxylic acid (ACC), L-tryptophan, tryptamine, and several cytokinin-related metabolites showed higher relative signals. Tryptophan metabolism was a shared enriched pathway in the integrated analysis. L-Tryptophan was positively correlated with Anthranilate synthase beta subunit 2 (ASB2) and negatively correlated with Tryptophan synthase alpha chain (TSA) and Probable indole-3-pyruvate monooxygenase (YUC) across the six samples; these exploratory correlations do not establish regulatory relationships. The observed patterns are consistent with coordinated changes in hormone-related metabolites, secondary metabolism, and gene expression during root enlargement. Because Indole-3-acetic acid (IAA) and lignin were not directly quantified, the study does not infer their concentrations or deposition. These findings provide a multi-omics resource for investigating tuberous-root development and for guiding future functional and targeted validation studies in this endangered medicinal species.
