From phylogeny to biotechnology: integrative genomic studies on Pleurotus eryngii and other fungal taxa

Fungal biodiversity represents a key component of terrestrial ecosystems and a promising source of biotechnological innovation. Yet, the genomic forces shaping diversity, adaptation, and functional potential within and among fungal species remain only partially understood. This doctoral thesis combines multigene phylogenetics, population genomics, and functional assays to investigate fungal variability across three taxa: Peziza spp., Tuber borchii Vittad., and Pleurotus eryngii (DC.) Quél. In the first part, we explored fine-scale genetic variation in a nivicolous Peziza species inhabiting a spatially restricted and environmentally extreme Alpine habitat. Using multigene analyses and sequence-based diversity metrics, we reconstructed intraspecific relationships and assessed whether micro-geographical isolation and selective pressures promote cryptic diversification. The second research axis focused on the Mediterranean truffle T. borchii, a species of high ecological and commercial relevance. Whole-genome resequencing of Sardinian and continental isolates enabled single-nucleotide polymorphism (SNP) discovery, principal component analysis (PCA), and F_ST- based genomic scans. Results revealed very low overall divergence (mean F_ST ≈ 0.008), supporting This finding may therefore reflect historical connectivity. The final part of the thesis concentrated on the edible and medicinal mushroom P. eryngii. We generated a genome-wide characterization of commercial strains, integrating SNP calling, Gene Ontology analysis, and the bioaccumulation assays of mycelia and fruiting bodies under heavy-metal exposure. Ethanol extracts of P. eryngii were also tested on hepatocarcinoma cell lines (Huh7 and HepG2), revealing antioxidant capacity and potential cytoprotective effects, supporting emerging nutraceutical applications. Taken together, this work provides an integrated view of fungal diversity, spanning evolutionary scales, biological and ecological contexts, and applied biotechnology highlighting how genomics can bridge knowledge gaps in fungal research and can improve sustainable exploitation of fungal resources.