Cyanidioschyzon merolae, an extremophilic unicellular red alga thriving in acidic hot springs at temperatures of 40–56 °C and pH 0.5–4.0, faces extreme oxidative stress conditions. This study presents a comprehensive genomic analysis of the carotenoid and vitamin E biosynthetic pathways, which are essential for antioxidant defense in this organism. Through comparative genomics using Arabidopsis thaliana sequences as queries, we identified and characterized genes encoding key enzymes involved in their metabolism. Our analysis reveals that C. merolae exclusively utilizes the methylerythritol-4-phosphate (MEP) pathway for isoprenoid biosynthesis and lacks a complete mevalonate (MVA) pathway. We identified eleven genes involved in terpenoid metabolism and seven genes specifically for carotenoid biosynthesis. Pigment analysis confirmed a streamlined carotenoid profile consisting solely of β-carotene, β-cryptoxanthin, and zeaxanthin, lacking the entire β,ε-branch and part of the β,β-branch. The complete tocopherol biosynthetic pathway produces exclusively α-tocopherol. The absence of the β,ε-carotenoid branch and the exclusive production of α-tocopherol demonstrate metabolic streamlining while maintaining antioxidant efficacy. These findings provide molecular blueprints for biotechnological applications, enabling targeted strategies to enhance antioxidant production through pathway optimization and metabolic engineering, while offering insights into developing stress-tolerant organisms and enhancing nutritional content in crops.

The billion-year-old fossil red alga Bangiomorpha pubescens represents the oldest taxonomically resolved multicellular eukaryote, morphologically indistinguishable from the extant intertidal alga Bangia fuscopurpurea. Here, we report a chromosome-level 107.55 Mb genome assembly of B. fuscopurpurea. Phylogenomic analysis confirms its placement as the most basal multicellular red algal lineage, diverging ∼973.40 million years ago. The genome reveals lineage-specific expansion of Osvaldo-type LTR retrotransposons that influence generation-specific gene expression. Metabolically, B. fuscopurpurea relies exclusively on the methylerythritol phosphate pathway for terpenoid biosynthesis, lacking the mevalonate pathway. Genomic analysis reveals the presence of core abscisic acid biosynthetic genes alongside some components of other hormone pathways, suggesting that fundamental phytohormone biosynthetic capacity was established in early red algal lineages. Multi-omics profiling reveals pronounced transcriptional and epigenetic differences between haploid gametophytes and diploid sporophytes, with distinct generation-specific DNA methylation patterns (5mC and 6mA). Time-series transcriptomic analyses identified 2,320 rhythmically expressed genes exhibiting diurnal patterns aligned with intertidal environmental fluctuations, including reactive oxygen species detoxification genes peaking at dusk and photoprotective genes at dawn. These findings illuminate the genomic innovations underlying early multicellular evolution, life cycle regulation, and intertidal adaptation in ancient red algae, establishing B. fuscopurpurea as a critical reference for understanding photosynthetic eukaryote diversification.