Dual omics comparison: how Agrobacterium tumefaciens and Agrobacterium rhizogenes modulate gene expression and metabolism in Hypericum perforatum L

Agrobacterium -mediated transformation is a fundamental method for the genetic modification of plants. However, several important crops and medicinal plants are recalcitrant to this process, hindering the application of modern functional genomics and genetic improvement tools. Hypericum perforatum L. (St. John’s wort), a valuable medicinal plant due to its secondary metabolites, is particularly recalcitrant to transformation mediated by Agrobacterium tumefaciens, and the molecular basis for this resistance remains unclear. This study was conducted to investigate the defense responses of H. perforatum after co-cultivation with A. tumefaciens and Agrobacterium rhizogenes through an integrative transcriptomic and metabolomic approach. Transcriptome profiling revealed extensive reprogramming of gene expression in response to both Agrobacterium strains. Core genes for signal transduction, defense responses, transcriptional regulation and biosynthesis of secondary metabolites were strongly differentially expressed. In particular, WRKY, MYB and ERF transcription factor-encoding genes were induced, reflecting their role in triggering plant immunity. The upregulation of genes related to xanthone biosynthesis and the associated downregulation of flavonoid metabolism genes indicate a metabolic Shift towards xanthone production. Metabolomic analyses consistent with these results showed a striking increase in defense-related xanthones such as 6-deoxyisojacareubin, hyperxanthone E and gemixanthone A after treatment with Agrobacterium. H. perforatum possesses a controlled defense response to Agrobacterium that involves the transcriptional induction of defense signals and the accumulation of antimicrobial xanthones. The suppression of flavonoid biosynthesis also indicates a redirection of resources towards more efficient defense compounds. These results are important to elucidate the molecular basis of recalcitrance of H. perforatum transformation and to identify the role of pre-existing and inducible immunity in limiting Agrobacterium-mediated gene transfer.