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.