Integrated Transcriptomic and Metabolomic Analyses Reveal Organ-Specific Molecular and Metabolic Features in Nitraria sibirica

Background/Objectives: Nitraria sibirica Pall. is a halophytic shrub with ecological and phytochemical value, but its organ-level molecular organization remains poorly resolved. Methods: We integrated RNA sequencing and untargeted LC–MS metabolomics for matched roots, stems, leaves, and fruits collected from one field population. Results: We quantified 25,263 genes and 2143 annotated metabolite entries, and the four organs separated clearly in both omics datasets. Across six pairwise comparisons, 12,160 nonredundant differentially expressed genes and 1446 nonredundant differentially accumulated metabolites were identified; intersection screening further resolved 3955 organ-preferential genes and 539 organ-preferential metabolites. Leaves contained the largest and most diverse preferential metabolite set and showed photosynthetic, chloroplast, pigment, and carbon-fixation signatures. Stems were distinguished by secondary-cell-wall, cytoskeletal, carbohydrate-conversion, phenylpropanoid, and lignan-related patterns. Fruits preferentially accumulated organic acids, amino-acid-related metabolites, sugars, and glycosides and showed energy-metabolism and flavonoid-modification signatures. Roots contained fewer preferential metabolites and were characterized by signaling, protective responses, RNA processing, and surface-barrier metabolism. WGCNA identified one significant organ-associated module for each organ, and cross-omics analyses linked these modules to preferential metabolites while prioritizing candidate gene–metabolite associations. Conclusions: These data define matched four-organ molecular and metabolic partitioning in N. sibirica and provide testable candidates for functional and targeted-metabolite validation.