Insulated Outlier Chromosomes Enable Metabolic Innovation in Minimal Eukaryotic Algae

How do organisms with compact genomes maintain evolutionary adaptability? Mamiellales, marine picoeukaryotes including Ostreococcus tauri , the smallest known free-living eukaryote, achieve ecological success despite severe genomic constraints. Using chromosome conformation capture (Hi-C) to investigate three-dimensional genome organisation in O. tauri , we reveal that two outlier chromosomes with low-GC regions are spatially insulated from the core genome, forming compartments akin to topologically associated domains. These compartments exhibit hypomethylation, altered nucleosome dynamics, and enrichment in transposable elements, introns, and highly expressed genes. They harbour polyketide synthase genes undergoing active structural diversification, with species-specific metabolite profiles including putative polyketides. This genomic architecture enables evolutionary experimentation while protecting essential functions, a strategy we demonstrate is convergently evolved in the distantly related picoeukaryote Pelagomonas . Our findings reveal that spatial compartmentalisation of adaptive processes represents a fundamental mechanism for maintaining evolutionary flexibility under genomic streamlining.