Widely targeted metabolomics of different tissues in Rubus corchorifolius

Abstract

Rubus corchorifolius, a medicinal plant of the Rosaceae family, is known for its diverse bioactive compounds. This study employs widely targeted metabolomics to investigate the metabolic profiles of leaf, stem, and flower tissue from R. corchorifolius. Using ultra-performance liquid chromatography coupled with tandem mass spectrometry, we identified 1,946 metabolites across the three tissue types. Multivariate statistical analyses revealed distinct metabolic signatures for each tissue, with flowers showing the most distinctive profile. Differential accumulation of flavonoids, phenolic acids, and primary metabolites reflected the specialised functions of each tissue type. Pathway enrichment analysis highlighted tissue-specific metabolic activities, including flavonoid biosynthesis in flowers and chlorophyll metabolism in leaves. This comprehensive metabolic characterisation provides a foundation for further investigations into the biosynthetic pathways and physiological functions of bioactive compounds in R. corchorifolius, potentially guiding future applications in medicine and agriculture.

Keywords: Rubus corchorifolius; medicinal plant; metabolic profiles; metabolomics; tissue-specific metabolism.

Figure 1

Metabolite profiling and analysis of different tissues in R. corchorifolius. (a) Distribution of main chemical classes among the detected metabolites. The pie chart illustrates the relative proportions of different metabolite classes, with flavonoids (26.31%) and phenolic acids (17.01%) being the most abundant. (b) Venn diagram showing the number of common and unique metabolites between RFl_vs_RFo (flower vs flower bud) and RFl_vs_RCa (flower vs calyx) comparisons; 724 metabolites are shared between the two comparisons. (c) PCA score plot of metabolite profiles in different tissues. Each point represents a sample, with colours indicating tissue types: RCa (green, calyx), RFo (orange, flower bud), RFl (purple, flower), and QC (pink, quality control). (d) OPLS-DA model validation by the permutation test. The graph shows the R2 and Q2 values for the original model (far right) and permuted models, indicating the model’s robustness and predictive power.

Figure 2

Hierarchical clustering heatmap of differential metabolites across tissues of R. corchorifolius. The heatmap displays the relative abundance of differential metabolites (rows) in different tissue samples (columns). The colour scale represents the Z-score normalised abundance, with red indicating high abundance and green indicating low abundance. Tissue types are labelled at the top: RCa (calyx), RFo (flower bud) and RFl (flower). The right-side bar shows the metabolite classes, revealing distinct accumulation patterns across tissues.

Figure 3

KEGG pathway enrichment analysis of differential metabolites between tissues of R. corchorifolius. (a) Bubble plot showing the top 20 enriched KEGG pathways. The x-axis represents the rich factor (ratio of differential metabolites to total metabolites in a pathway), and the y-axis lists the pathway names. Bubble size indicates the count of differential metabolites, while the colour represents the p-value (red: more significant, blue: less significant). (b) Heatmap of key differential metabolites involved in enriched pathways. Rows represent individual metabolites, and columns represent different tissue samples (RFl: flower, RCa: calyx). The colour scale indicates the relative abundance of metabolites (red: high, green: low).