All About Bias : Researching adaptation and genome composition in filamentous fungi

Fungi play key roles in nutrient cycling, symbioses, and as sources of industrially and medically relevant compounds. Yet, major gaps persist in our knowledge of how fungal genomes evolve and adapt, including in economically and ecologically important lineages such as the Sordariales order. By combining phylogenomics, comparative genomics, and laboratory experiments, this thesis addresses these gaps and advances knowledge of fungal evolutionary biology. In Chapter 1, we generated a genome-wide phylogeny of 99 Sordariales species, including 52 newly sequenced genomes, which allowed us to resolve previously ambiguous family relationships. We showed that major families in the order differ in genome size, GC content, and gene number, with these differences arising primarily through within-family evolution. Chapter 2 built on this framework and analysed codon usage bias in conserved coding sequences from the Sordariales dataset. These analyses revealed variation in codon usage bias and selection strength across families. Within the order, the Chaetomiaceae family exhibits stronger codon bias and selection on codon usage than the Podosporaceae and Sordariaceae families. We hypothesize that this high codon bias in Chaetomiaceae could be linked to ecological niche specialization. Focusing on Chaetomiaceae, Chapter 3 revealed correlations between genomic traits and high optimal growth temperatures in fungi. Fungi with optimal growth temperatures ≥ 45 °C showed elevated nucleotide and amino acid substitution rates, increased strength of purifying selection, reduced genome sizes, and increased GC content compared to mesophilic relatives. Extending from the Sordariales to the order Hypocreales, Chapter 4 examined heavy metal adaptation in six Fusarium species isolated from the Kiirunavaara mines in Northern Sweden. We found that mine isolates displayed higher metal tolerance but lower uptake than isolates from non-contaminated sites, indicating an adaptive trade-off between the two traits. Metal tolerance varied by heavy metal, and followed the order of zinc > copper > iron. Additionally, species-specific differences were observed, suggesting that bioremediation potential is species dependent, in addition to the effect of environment origin. Overall, the work in this thesis advances our understanding of how fungal genomes evolve. It highlights the diverse strategies by which fungi adjust to environmental challenges and underscores the power of integrating phylogenomic approaches with genome-wide comparative analysis to help uncover the mechanisms that shape fungal evolution.