GRAS transcription factors are essential for plant growth and stress adaptation, yet they remain uncharacterized in the medicinal herb Coptis chinensis. To address this gap, we performed a genome-wide identification of the GRAS family and investigated its transcriptional responses to temperature and light stress, integrating comparative transcriptomics with promoter analysis to explore potential co-expression with bZIP factors. A total of 48 CcGRAS genes were identified and found to be unevenly distributed across nine chromosomes. Expression profiling revealed that CcGRAS genes are markedly more responsive to varying light intensities (476, 8340 lx) than to temperature stresses (15, 35 °C), relative to controls (2060 lx for light, 25 °C for temperature). Co-expression analysis uncovered an underground tissue-specific module in which CcbZIP16 is upregulated with four CcGRAS genes (CcGRAS11, CcGRAS12, CcGRAS43, CcGRAS48) that are coordinately upregulated specifically under low-light conditions. The promoters of these co-expressed genes are significantly enriched in canonical light-responsive cis-elements, providing correlative evidence for their coordinated transcriptional control. Together, these findings identify a tissue-specific GRAS-bZIP co-expressed gene set under light stress and suggest a candidate regulatory framework for dissecting light adaptation mechanisms. This work also provides a foundation for targeted genetic improvements in stress tolerance and alkaloid biosynthesis in this important medicinal plant.

The basic leucine zipper (bZIP) transcription factors play crucial roles in plant growth and stress adaptation. However, a comprehensive genome-wide analysis of this family has been lacking in the medicinal plant Coptis chinensis. In this study, we identified 55 bZIP genes (CcbZIPs) from the C. chinensis genome and systematically classified them into 12 subfamilies through phylogenetic analysis with Arabidopsis thaliana. Notably, subfamilies L and O were absent, while two orphan genes were discovered, indicating lineage-specific evolution. Expression profiling revealed that numerous CcbZIPs respond dynamically to temperature and light stresses in a tissue-specific manner. These findings provide a foundation for understanding the regulatory roles of CcbZIPs in environmental adaptation and secondary metabolism, offering potential genetic targets for future breeding aimed at improving stress tolerance and medicinal compound production in C. chinensis.

The medicinal and edible plant Gardenia jasminoides is attracting attention as a source of natural food-active components. Integrated GC–MS/LC-MS metabolomics revealed that G. jasminoides fruits specifically accumulate bioactive triterpenoids, including the GRAS antioxidant squalene (220 ng/mg FW) and methyl oleanonate, a compound with reported anticancer (PPARγ agonist) activity. As the central biosynthetic hub, GjSQS showed fruit-predominant expression, strongly correlating with triterpenoid abundance. Functional validation confirmed its ER localization and efficient in vitro conversion of FPP to squalene. The dual-ionization LC-MS approach revealed tissue-partitioned acidic triterpenoids that were undetectable using single ionization modes, enhancing the comprehensiveness of metabolomic profiling. These findings underscore G. jasminoides fruits as a sustainable source of food-active triterpenoids and establish GjSQS as a key metabolic engineering target. Its expression in food-grade microbial chassis offers a promising strategy to enhance the production of high-value triterpenoids for functional foods and additives.