Light quality rewires module–trait networks in Euglena gracilis to drive carotenoid and paramylon accumulation

Background Light quality is a critical and tractable parameter for directing carbon partitioning in microalgae toward the synthesis of high-value bioproducts. In this study, Euglena gracilis was employed as a model photosynthetic system to investigate spectral regulation of bioproduct accumulation. An integrative approach combining physiological measurements, quantification of major bioproducts (including chlorophylls, carotenoids, lipids, protein, and the β-1,3-glucan paramylon), and RNA-sequencing-based weighted gene co-expression network analysis (WGCNA) was used to dissect spectrum-specific regulatory programs. Results Distinct spectral treatments induced divergent photochemical responses ( Fv / Fm ) and bioproduct profiles. WGCNA identified 12 transcriptional modules, which were correlated with specific traits and treatments using module eigengene analysis. One module, enriched in carotenoid biosynthesis genes, showed a strong positive correlation with total carotenoid content ( r ≈ 0.85, p < 0.001). A separate module associated with photosystem function and photoprotection closely tracked changes in Fv / Fm ( r ≈ 0.75, p ≈ 0.03). Notably, a third module responsive to blue-light-dominant conditions displayed positive correlations with chlorophyll a, carotenoids, and paramylon (| r | ≈ 0.74–0.79; p < 0.05), suggesting an integrated regulatory axis linking light perception, photosynthetic performance, and carbon storage. Additional modules correlated with protein accumulation and broad-spectrum (white) light exposure, implicating coordinated regulation of translational capacity and cytoskeletal dynamics. Conclusions Collectively, these module–trait associations elucidate how light quality orchestrates plastidial function, redox homeostasis, isoprenoid biosynthesis, and β -1,3-glucan metabolism to reprogram bioproduct yields. This network framework identifies candidate pathway regulators and provides strategic insights for optimizing spectral conditions to enhance carotenoid and paramylon production in E. gracilis , supporting advanced microalgal biorefinery development.