Decoding the Chemodiversity blueprint: Chromosome-scale genome assembly unveils photosynthesis-terpenoid coordination in Cinnamomum burmanni through genomic and miRNA regulatory networks

The intricate interplay between photosynthetic efficiency and terpenoid biosynthesis in plants remains a pivotal yet underexplored area in secondary metabolism research. This study elucidates the physiological and molecular mechanisms underlying this synergy in Cinnamomum burmanni, a chemically diverse Lauraceae species, through a multi-omics approach. A high-quality chromosome-level genome of C. burmanni (1.14 Gb, scaffold N50: 94.90 Mb) was assembled, and evolutionary analyses revealed species-specific gene family expansions, particularly in mono-, sesqui-, and diterpenoid biosynthesis pathways. Comparative analyses of photosynthetic traits across chemotypes demonstrated that the borneol-type exhibits superior photosynthetic capacity, characterized by elevated net photosynthetic rate, transpiration rate, stomatal conductance, intercellular CO₂, carboxylation efficiency and non-photochemical quenching. The phenotype is linked to upregulated chlorophyll metabolism, carotenoid biosynthesis regulators, and enhanced light-harvesting complex and photosystem components, optimizing light energy conversion. Mechanistically, photosynthetic activity modulates precursor flux into terpenoid pathways by regulating rate-limiting enzymes. Additionally, lineage-specific expansions of terpene synthase and isopentenyl diphosphate synthase gene families underpin specialized terpenoid production. A post-transcriptional regulatory network involving 14 miRNAs (e.g., miR396, miR2950) was identified, coordinately targeting 11 key genes in both photosynthesis and terpenoid synthesis, suggesting a dual role in metabolic fine-tuning. This work advances understanding of the evolutionary and physiological integration of photosynthesis and secondary metabolism in aromatic plants, offering a genomic foundation for biotechnological applications in metabolite synthesis and chemotype breeding.