Multi-Omics Decoding of Fucoxanthin Biosynthesis: a Roadmap for Rational Synthetic Pathway Design

Fucoxanthin is a marine xanthophyll with exceptional antioxidant, photoprotective and clinically relevant bioactivities, making it a flagship target for next‑generation microalgal biomanufacturing. However, low natural productivities, incomplete knowledge of its biosynthetic regulation and the empirical nature of current strain‑improvement strategies continue to limit industrial translation. In this review, we make recent advances across genomics, transcriptomics, proteomics, metabolomics and epigenomics that collectively decode the molecular architecture and regulatory logic of fucoxanthin biosynthesis in diatoms, haptophytes and related marine microalgae. Comparative and evolutionary genomics delineate conserved scaffolds of the methylerythritol phosphate (MEP) pathway and lineage‑specific expansions of key carotenogenic genes such as dxs, psy, zep and vde). At the same time, transcriptome and chromatin‑state maps reveal how light, nutrients, temperature and redox cues dynamically rewire fucoxanthin gene networks. Proteo‑metabolomic studies validate these regulatory nodes at the enzyme and metabolite levels, uncovering multi‑enzyme complexes, cofactor bottlenecks and cross‑talk with chlorophyll biosynthesis that together govern pathway flux. Integrating these omics layers with genome‑scale metabolic models, kinetic simulations and artificial‑intelligence‑driven network inference enables predictive identification of control points and in silico design of high‑flux fucoxanthin modules. We further highlight emerging synthetic‑biology strategies including CRISPR‑based genome and epigenome editing, modular multi‑gene circuit design, optogenetic and NADPH‑responsive control systems and hybrid algal bacterial consortia that translate multi‑omics insight into rational pathway engineering. Further, we outline how digital‑twin photobioreactors, techno‑economic assessments and life‑cycle analyses can couple omics‑optimized strains to scalable, circular blue‑bioeconomy processes. Together, this multi‑omics and systems‑engineering roadmap establishes a rational foundation for next‑generation fucoxanthin cell factories and provides a generalizable paradigm for marine metabolic engineering.