Multi-omics reveals organ-specific sinomenine biosynthesis and endophyte-mediated modulation in dioecious Sinomenium acutum

Sinomenium acutum accumulates bioactive benzylisoquinoline alkaloids (BIAs), especially sinomenine, yet the spatial organization of BIA biosynthesis across organs and the contribution of endophytic microorganisms remain unclear. Here, we integrated untargeted and targeted metabolomics, transcriptomics, and 16S rRNA/ITS amplicon sequencing to characterize BIA accumulation and microbiome-metabolite associations in roots, stems, and leaves of female and male plants. Sex-related metabolic differences were generally weak, with only a few BIA-related metabolites, including harringtonine, sanguinarine, and corynoline, showing significant differences in specific organs; sinomenine showed a sex-related trend but no significant difference. By contrast, roots, stems, and leaves exhibited pronounced metabolic divergence. Upstream BIA precursors, including L -tyrosine, dopamine, and 4-hydroxycinnamic acid, were relatively enriched in aboveground organs, whereas downstream BIAs, including (S)-reticuline, sinoacutine, (S)-scoulerine, and sinomenine, accumulated predominantly in roots. Transcriptomic analysis supported an organ-partitioned model: genes encoding enzymes involved in precursor biosynthesis, including PAT, ASP5, and EC 1.10.3.1, were highly expressed in leaves; genes encoding NCS and BBE1, associated with midstream BIA conversion, were enriched in stems; and genes encoding CYP80B1 and CNMT, involved in downstream modification, were highly expressed in roots. Microbial communities showed weak sex-related differences but clear tissue-associated patterns. Fungal taxa showed more consistent associations with BIA-related metabolites than bacteria. Notably, Cladosporium -related taxa were associated with multiple BIA metabolites, and root irrigation with the leaf-derived endophytic fungus P37 ( Cladosporium tenuissimum ) significantly promoted root sinomenine accumulation. These findings reveal an organ-centered regulatory framework for BIA biosynthesis in S. acutum and highlight endophytic fungi as potential resources for improving sinomenine production.