A Comprehensive Analysis of Transcriptomics and Metabolomics Reveals Key Genes Involved in Terpenes Biosynthesis Pathway of Litsea cubeba Under Light and Darkness Treatments

Light is an important environmental regulator of plant secondary metabolism. Terpenoids, the most abundant secondary metabolites in plants, demonstrate a wide spectrum of biologically significant properties, encompassing antimicrobial, antioxidative, and analgesic activities. <i>Litsea cubeba</i> (Lour.) Pers., a core species within the Lauraceae family, exhibits notable pharmacological potential, including antimicrobial and antitumor effects. Here, we found that darkness treatment significantly suppressed terpenoid accumulation in <i>L. cubeba</i> fruits. To clarify the molecular mechanisms underlying the regulatory effect of light and darkness treatments on terpenoid biosynthesis, we conducted a comparative transcriptome profiling of <i>L. cubeba</i> fruits under light and darkness treatments. A total of 13,074 differentially expressed genes (DEGs) were identified among four sampling time points (L1-L2-L3-L4 vs. D1-D2-D3-D4). These genes were enriched in various pathways, with significant enrichment being observed in the terpenoid and other secondary metabolism pathways. Additionally, the enrichment of DEGs in L2 and D2 stages was further studied, and it was found that nine DEGs were significantly enriched in the monoterpene synthesis pathway. The weighted gene co-expression network analysis (WGCNA) showed that alcohol dehydrogenase (<i>ADH</i>), a key enzyme in terpenoid synthesis, had the same expression pattern as <i>WRKY</i> and <i>NAC</i> transcription factors, suggesting their involvement in the biosynthesis of terpenoids in <i>L. cubeba</i>. Expression profiling demonstrated that plastid-localized terpenoid pathway genes were markedly downregulated under darkness treatment. qRT-PCR validation of key genes (<i>LcDXS3</i>, <i>LcHMGS1</i>, <i>LcMDS</i>, and <i>LcTPS19</i>) confirmed the reliability of the transcriptome data, with <i>LcDXS3</i> exhibiting pronounced declines in expression after 6 h (2.76-fold decrease) and 12 h (2.63-fold decrease) of darkness treatment. These findings provide novel insights into the photoregulatory mechanisms governing terpenoid metabolism in <i>L. cubeba</i>.