Insights into the Adaptive Evolution of Cinnamomum burmanni Through TMT Proteomic and RNA-Seq Analyses

Cinnamomum burmanni (Nees & T. Nees) Blume, a member of the Lauraceae family, exhibits adaptability to diverse environmental conditions by synthesizing a diverse array of specialized secondary metabolites, including terpenoids and cinnamaldehyde. Nevertheless, the molecular mechanisms underlying the chemical diversity in the leaves of C. burmanni and their remarkable adaptation to subtropical and tropical forests in South China have not been thoroughly investigated. This research integrates transcriptomic and proteomic analyses across five chemotypes of C. burmanni, namely, the borneol-type (BORCB), cinnamaldehyde-type (PROCB), eucalyptol-type (EUCCB), phytol-type (PHYCB), and chlorophyllinol-type (CARCB), by means of the Nanopore and Nano UPLC-MS/MS sequencing data. The findings indicate that PROCB demonstrates an up-regulation of the phenylpropanoid pathway (such as PAL, C4H, PR proteins), which is associated with biotic stress defense. In contrast, the terpenoid-dominated chemotypes (BORCB, EUCCB, PHYCB) prioritize the biosynthesis of monoterpenes and diterpenes as well as redox homeostasis. Protein–protein interaction networks highlight functional specialization; BORCB up-regulates the expression of enzymes GGPPS and TPS2, which are involved in monoterpene production; PHYCB enhances the activity of diterpene synthases (CPS, KSL) and chloroplast retrograde signaling; EUCCB activates SOD/GST to mitigate oxidative stress. PROCB induced defense hubs (NPR1, WRKY33) mediated by salicylic acid and pathogenesis-related proteins. The study establishes a comprehensive multi-omics resource for a gene–protein–metabolite framework, elucidating the mechanisms of stress resilience of C. burmanni in South China.