Rhizome differentiation is associated with metabolic specialization and rhizosphere microbial assembly in Rheum...

Distinct rhizome architectures are associated with differences in metabolic profiles and rhizosphere microbial composition within a single plant. Rhizome differentiation is a common developmental feature in perennial medicinal plants, yet its association with secondary metabolism and rhizosphere microbial assembly remains poorly understood. Here, we investigated the functional divergence between main rhizome (DH) and lateral rhizome (DC) of Rheum officinale Baill. using integrated metabolomic and transcriptomic analyses, quantitative real-time PCR (qRT-PCR) validation, and rhizosphere microbiome analyses. Metabolomic profiling revealed distinct patterns in anthraquinone allocation among rhizome types. DC exhibited a higher relative abundance of total detected anthraquinones and was enriched in both free anthraquinones (e.g., rhein) and selected glycosylated anthraquinones (e.g., chrysophanol 1-tetraglucoside), whereas DH preferentially accumulated other glycosylated metabolites such as cassiaside B2. Transcriptomic analysis identified 484 differentially expressed genes (DEGs) associated with these metabolic differences. Genes involved in anthraquinone biosynthesis and modification, including polyketide synthase (PKS), cytochrome P450 (CYP450), O-methyltransferase (OMT), and UDP-glycosyltransferase (UGT) family members, exhibited differential expression patterns associated with rhizome type, which were further validated by qRT-PCR. Although overall rhizosphere microbial diversity showed no significant differences between rhizome types, specific taxonomic shifts were observed, with Stenotrophomonas enriched in DC and Bacilli enriched in DH. Integrated analysis indicated correlation patterns among rhizome architecture, anthraquinone metabolism, transcriptional variation, and rhizosphere microbial composition. However, the directionality and underlying mechanisms of these relationships remain unresolved and warrant further mechanistic investigation. This study provides new insights into the biological basis of rhizome differentiation in Rheum officinale Baill.