Bioinformatic Analysis of Genomic and Transcriptomic Variation in Fungi

Fungi are microorganisms whose astounding variety can be found in every conceivable ecosystem on the planet. Fungi are nutrient recyclers, playing an irreplaceable role in the carbon cycle. They grow on land and in the sea, on plants and animals and in the soil. They feed us as mushrooms, and drive our economy as bioreactors. They leaven our bread and brew our beer, nourish our crops and spoil our food. They even directly play a role in human health. Fungi are, however, far more complex organisms than their simple phenotypes lead us to believe. In order to harness the potential of fungi, and to address the threats they pose, we must gain a better understanding of fungi. However, their substantial genomic and regulatory diversity impede our reasoning. Thus, to understand fungi, we need to understand their genetic and regulatory diversity.In this thesis, I developed and utilized bioinformatics methods to understandvariation within and between fungi. We focussed on two fungi: Agaricus bisporus (the champignon, or white button mushroom) because of commercial interest, and Schizophyllum commune (the split-gill mushroom) because it is used as a model organism for mushroom formation (for, amongst others, A. bisporus).Pattern Recognition and Bioinformatic