Co-Analysis of Metabolomics and Transcriptomics Reveals Key Pathways and Genes Associated with Pigment and Flavonoid Regulation in Mint

Metabolome and transcriptome landscapes reveal potential genes and metabolites involved in formation of leaf color in red-leafed apple mutants

Leaf color mutations in plants serve as valuable resources for investigating metabolic pathways related to biosynthesis of chlorophyll, flavonoid, and carotenoid. In this study, a comprehensive analysis of the physiological characteristics, transcriptomes, and metabolomic profiles of a mutant of Malus hupehensis var. pingyiensis with red leaves (RM) and normal plant (CK) with green leaves was performed. A total of 283 differentially abundant metabolites (DAMs) and 9,822 differentially expressed genes (DEGs) were identified between RM and CK. Compared with the CK, RM presented a reduced chlorophyll content and elevated levels of carotenoids, flavonoids, and anthocyanins. KEGG pathway enrichment analysis revealed that the DAMs and DEGs were associated mainly with the metabolism of chlorophyll, carotenoids, and flavonoids, with the anthocyanidin biosynthesis pathway showing the greatest enrichment. Several key anthocyanin biosynthetic genes, including chalcone isomerase (CHI), dihydroflavonol 4-reductase (DFR), UDP-Glucose:Flavonoid 3-O-Glucosyltransferase (UFGT), and UDP-glycosyltransferases (UGT), were upregulated in the red leaves, in line with a significant increase in cyanidin 3-O-glucoside (C3G) and pelargonidin 3-O-glucoside (pg3G). Furthermore, RNA sequencing (RNA-seq) analysis revealed upregulation of MdMYB10 and MdUFGT. Yeast one-hybrid (Y1H), chromatin immunoprecipitation (ChIP), and dual-luciferase reporter (LUC) assays demonstrated that MdMYB10 bound to the MdUFGT promoter fragment and subsequently upregulated its expression, leading to the accumulation of C3G and pg3G in RM. Our findings provide new insights into the regulatory mechanisms of leaf coloration and offer a foundation for the development of new cultivars with alteration of leaf color.

Integrated transcriptome and metabolome analysis reveals key genes and metabolic pathways regulating growth and development in Polygonatum cyrtonema Hua

Polygonatum cyrtonema Hua is a traditional Chinese medicine with the same origin as both medicine and food, and its medicinal components have considerable clinical value. Due to its substantial market demand, it is now primarily produced through artificial cultivation. To produce high-quality P. cyrtonema , we performed transcriptome and metabolome sequencing of one-year-old and three-year-old P. cyrtonema to explore the growth regulation mechanisms and key genes involved in improving its quality. A total of 1,957 differentially expressed genes (DEGs) and 163 differentially expressed metabolites (DEMs) were identified in this study. Integrated transcriptomic and metabolomic analyses suggested that the growth regulation of P. cyrtonema may be primarily associated with sphingolipid metabolism, phenylpropanoid biosynthesis, and starch and sucrose metabolism. Our data suggest that sucrose transport to sink organs may be facilitated by increased expression of the bidirectional sugar transporter SWEET14 , and sucrose may be hydrolyzed by β-fructofuranosidase , potentially providing energy for plant growth on one hand and contributing to fructose accumulation on the other. Furthermore, the elevated abundance of L-phenylalanine may be associated with an increase in secondary metabolites, which could provide a metabolic basis for age-dependent growth and metabolite partitioning in rhizomes. The observed downregulation of sphingolipid metabolism-related genes may reflect the perennial growth habit of P. cyrtonema , whereby slower growth in the first year may promote sphingolipid-mediated root development. However, we emphasize that these inferences are based on correlative transcriptomic and metabolomic data, and functional validation is required to establish causal relationships.

Comparative metabolomic and transcriptomic profiling of flavonoid diversity and antioxidant capacity in three Isatis species.

Flavonoids are key bioactive compounds in plants with significant health benefits. This study employs an integrated multi-omics approach to investigate flavonoid diversity and antioxidant capacity across three Isatis species: I. oblongata, I. tinctoria, and I. indigotica. Metabolomic profiling identified 200 flavonoids, with glycosides being the most abundant class. I. tinctoria exhibited the highest total flavonoid content and antioxidant activity, strongly correlated with the accumulation of 53 core differential flavonoid metabolites, most of which were glycosylated derivatives. Transcriptomic analysis revealed coordinated upregulation of phenylpropanoid pathway genes and specific UDP-glycosyltransferases (UGTs) in I. tinctoria, providing a genetic basis for its enhanced glycoside production. The study establishes a clear genotype-metabolite-phenotype linkage, highlighting glycosylation as a key mechanism underlying flavonoid-driven antioxidant superiority in Isatis. Although the current evidence is primarily correlative, the consistent and strong associations across independent transcriptomic, metabolomic, and antioxidant datasets provide a robust foundation for this conclusion. These findings offer new insights into the metabolic evolution and regulatory networks of flavonoids, with implications for breeding and metabolic engineering of high-value medicinal plants.

Multi-omics dissection of metabolic pathways for differential flavonoid accumulation in Solanum pennellii and S. lycopersicum

Unraveling the Metabolic Basis of Quality Divergence in White and Yellow Qamgur (Brassica rapa L.) During Growth Through Comparative Metabolomics

Qamgur is a widely consumed vegetable and is also used in traditional medicine because of its extensive health benefits. White and yellow are the two main varieties. However, the mechanisms underlying quality development in these varieties, particularly in yellow Qamgur, remain unclear. This study compared nutritional and functional components throughout development. Total phenols and total isothiocyanates showed similar trends and levels in both varieties, whereas total free amino acids showed related but distinct patterns. Yellow Qamgur accumulated significantly higher levels of carotenoids. The integrated use of widely targeted and targeted metabolomics revealed stage-specific metabolites. White Qamgur showed stronger enrichment in secondary metabolite pathways, such as anthocyanin, flavonoid, steroid, terpenoid, and phenylpropanoid biosynthesis. In contrast, yellow Qamgur showed stronger enrichment in primary metabolic pathways, including amino acid biosynthesis. In addition, carotenoid biosynthesis may be the primary pathway responsible for the yellow coloration. Carotenoid profiling revealed that lycopene (28.94 mg/kg) was the predominant carotenoid in yellow Qamgur, followed by violaxanthin, γ-carotene, phytoene, β-cryptoxanthin laurate, and β-carotene.

Integrated Analysis of Metabolome and Transcriptome Provides New Insights into the Genetic Basis Underlying the Regulation of α-Linolenic Acid Biosynthesis in Perilla frutescens Seeds

Perilla (Perilla frutescens) is an important oil-bearing crop rich in α-linolenic acid (ALA), and seed oil quality varies greatly among different germplasms. However, the molecular and metabolic mechanisms underlying genotypic differences in ALA accumulation remain unclear. In this study, four Perilla varieties with distinct seed phenotypic traits were used to investigate the variations in seed quality, metabolome, and transcriptome. Significant genotypic differences were observed in seed color, thousand-grain weight, and oil content. QO8 showed the highest seed oil content, while QS5 and QO10 exhibited relatively lower oil accumulation levels. Metabolome analysis revealed that lipid metabolism was the dominant metabolic category in Perilla seeds. Multiple differentially accumulated metabolites (DAMs), including ALA, stearic acid, traumatic acid, and 10-OPDA, displayed genotype-specific accumulation patterns. KEGG enrichment demonstrated that α-linolenic acid metabolism and unsaturated fatty acid biosynthesis were the most significantly divergent pathways among different Perilla germplasms. Transcriptome analysis identified numerous differentially expressed genes (DEGs) involved in fatty acid and ALA biosynthesis, such as FAD2, LOX, AOS, AOC, OPR, KAT, ECH, and ACOX. Integrated transcriptome and metabolome analysis further confirmed that the differential expression of structural genes altered the metabolic flux of the ALA and downstream jasmonic acid pathway, resulting in varied accumulation of core lipid intermediates. In addition, WRKY and MYB transcription factors were identified as key upstream regulators that positively or negatively modulated ALA metabolic homeostasis. This study systematically clarified the phenotypic, metabolic, and transcriptional differences in seeds of different Perilla varieties and revealed the core regulatory network of ALA biosynthesis. These findings provide valuable candidate genes and a theoretical foundation for elucidating the molecular mechanism of high ALA accumulation and quality improvement in Perilla seeds.