Integration of transcriptomics and metabolomics provides insights into secondary cell wall deposition and terpenoid biosynthesis during stem development in Camphora officinarum.

Camphora officinarum Nees (Cinnamomum camphora) has traditionally been cultivated as bushes for essential oil extraction from its leaves and twigs (small stems). terpenoid deposition in leaves is well-studied, While the stems have received less attention. Using the camphor tree reference genome, we profiled stem transcriptomes and metabolomes across four developmental stages in linalool- and borneol-type camphor trees to elucidate key genes underlying secondary cell wall deposition and terpenoid biosynthesis. Weighted Gene Co-expression Network Analysis (WGCNA) highlighted enrichment of phenylpropanoid and starch and sucrose metabolism pathways, consistent with active secondary cell wall formation. Expression of the full complement of lignin biosynthesis genes, including those participating in non-conserved bypass routes (e.g., CSE, C4H, and C3'H), indicated chemotype-specific timing of lignification (earlier in the linalool-type). Across development, downshifts in GPPS, FPPS, and GGPPS expressions were observed in both chemotypes, whereas their precursor supply appeared to favor distinct routes: DXS (MEP pathway) was identified in the linalool-associated co-expression modules, while HMGCR (MVA pathway) was identified in the borneol-associated modules; elevated ACAT further typified the borneol-type. Regulatory programs also diverged: WGCNA associated brassinosteroid-linked genes with the linalool-type and cytokinin-linked genes with the borneol-type; comparative analysis revealed that ERF026 and SHR2 were upregulated in the linalool-type, whereas bHLH068, bHLH093, and WRKY40 were upregulated in the borneol-type. Overall, these findings provide insights into lignocellulosic biomass formation and terpenoid biosynthesis during stem development, highlighting key drivers of chemotype diversity in C. officinarum.