Evolution of carotenoid biosynthesis genes in the eustigmatophyte alga Vischeria sp. NIBR-HCW20 (Stramenopiles)

Eustigmatophyte algae (Stramenopiles) contain a relatively small complement of pigments (e.g., chlorophyll a , zeaxanthin, violaxanthin, and vaucheriaxanthin ester) compared with other photosynthetic stramenopiles. The carotenoid biosynthesis pathway in algae proceeds sequentially through the non-mevalonate pathway, the geranylgeranyl diphosphate (GGPP) pathway, phytoene and lycopene synthesis, and the cyclization and hydroxylation of xanthophylls. Several gene families, including GGPPS, GGPS1, FPPS, and GPPS, are involved in the GGPP pathway. However, these gene families are widely distributed across diverse eukaryotes, and their evolutionary histories are incompletely understood. Carotenoid isomerase (CrtISO) functions in the final step of lycopene synthesis but is absent in stramenopiles. Several CrtISO-like genes, including a functional homolog of CrtISO are present in diatoms, but their distribution in other stramenopiles is unknown. In this study, we generated a high-quality genome assembly of the eustigmatophyte Vischeria sp. NIBR-HCW20 (JBVFKS000000000) and analyzed its carotenoid biosynthesis pathway. We reconstructed the evolutionary history of genes in the GGPP pathway, demonstrated independent diversification of CrtISO-like genes, and identified species-specific duplications of LHC/VCP genes in NIBR-HCW20. Although the NIBR-HCW20 strain used for this study has been lost, its genome assembly provides a valuable resource for investigating the evolution of carotenoid biosynthesis and the consequences of gene duplication in this lineage.