Integrated Comparative Genomics and Structuromics Uncover Functional Adaptations and Conserved Autophagy in Three Pleurotus Species

The genus Pleurotus comprises economically important edible fungi with diverse ecological adaptations, yet the molecular basis of their functional diversity remains unclear. Comparative genomics of three Pleurotus species (Pleurotus ostreatus, Pleurotus citrinopileatus, Pleurotus salmoneostramineus) revealed species-specific gene expansions: reproduction/cell cycle in P. ostreatus, secondary metabolism in P. citrinopileatus, and amino acid/protein metabolism in P. salmoneostramineus. Laccase genes varied markedly in number and sequence, whereas chitin synthases were more conserved. Autophagy-related genes (17, 16, and 15, respectively) were identified. Structuromics uncovered species-specific secondary structures of laccases and chitin synthase dimer interfaces, which may reflect structural variations potentially linked to their distinct thermal niches. Remarkably, core ATG protein complexes exhibited highly conserved tertiary structures and interaction interfaces, with subtle modifications in ATG9 trimers. Comparative structuromics thus complements genomics by showing how structural variation in growth-related genes may underlie environmental plasticity, while also speculating the deep functional conservation of core machineries.