Integrated Metabolome and Transcriptome Analyses Reveal Candidate Regulatory Networks of Anthocyanin Biosynthesis in Cinnamomum burmanni (Nees et T. Nees)

Cinnamomum burmanni (Nees et T. Nees) Blume represents an economically valuable evergreen arbor celebrated for its essential oils; nevertheless, its floral and foliar anthocyanin metabolic profile remains largely uncharacterized. In this investigation, integrated LC-MS/MS-based targeted metabolomics, comparative RNA sequencing, weighted gene co-expression network analysis (WGCNA), and RT-qPCR validation were employed across mature foliage, floral buds, and anthesis flowers (designated YXYZD, YXHBD, and YXHDD, respectively). Metabolomic profiling resolved 49 flavonoid-related metabolites, including anthocyanin derivatives, other flavonoids, and procyanidins, spanning eight subclasses. We detected 37, 34, and 13 differentially accumulated metabolites (DAMs) in YXYZD vs. YXHBD, YXYZD vs. YXHDD, and YXHBD vs. YXHDD, with the anthocyanin biosynthetic pathway demonstrating prominent enrichment during floral transition. Concurrently, transcriptome profiling annotated 37,236 unigenes and captured 46 differentially expressed structural genes (DEGs) underpinning anthocyanin generation, including 5 PAL (phenylalanine ammonia-lyase), 1 C4H (cinnamate 4-hydroxylase), 7 4CL (4-coumarate-CoA ligase), 8 CHS (chalcone synthase), 1 CHI (chalcone isomerase), 10 F3H (flavanone 3-hydroxylase), 5 DFR (dihydroflavonol 4-reductase), 1 F3′5′H (flavonoid 3′,5′-hydroxylase), 2 ANS (anthocyanidin synthase), 5 BZ1 (anthocyanidin 3-O-glucosyltransferase), and 1 UGT75C1 (UDP-glycosyltransferase 75C1), whereas ANS showed dominant expression across bud and flower stages, contrasting with the leaf-restricted profile of UGT75C1. Network analysis resolved 22 expression modules (excluding the grey module), identifying candidate module–trait associations wherein the red and yellow clusters aligned tightly with cyanidin and delphinidin conjugates. Furthermore, expression divergence across 35 MYB and 14 bHLH transcription factors underscored their putative regulatory engagement. Joint transcript–metabolite integration highlighted BZ1 (EVM0001658) as a candidate key gene whose expression tracked cyanidin-3-O-rutinoside and delphinidin-3-O-sophoroside accumulation alongside down-regulation through flower opening. These data provide a foundation for understanding anthocyanin formation in C. burmanni and may facilitate future germplasm characterization and utilization.