Abstract
Fungi are a key component of ecosystem functioning, through their control of vital ecosystem processes like carbon storage and nutrient recycling, and their direct impact on plant and animal community structure through pathogenic or mutualistic interactions. They also impact, in a positive or negative manner, a host of human activities. Fungi can interact with many organisms, including myco-pathogens and myco-parasites. Microbes with the ability to exploit or kill fungi are widely distributed across the tree of life, and can be found in viruses, bacteria, nematodes, protists, arthropods and other fungi. Fungi seem to be able to regulate interactions with antagonistic microbes by mounting an immune response in a way similar to what has been identified in plants and animals. Mechanisms underlying the production of antagonistic metabolites are relatively well-known and the mode of action of a number of loci involved in the recognition of conspecific non-self has been deciphered. A hypothesis is that conspecific recognition processes, like vegetative or sexual incompatibility, are actually a byproduct of heterospecific (i.e. pathogen) non-self recognition. Under this hypothesis, there would be a unifying, and general system, involved in the sensing and response to non-self sensu lato in fungi. Plants and animals use Pattern Recognition Receptors (PRRs) to sense microbial cells. These proteins recognize specific molecular patterns and initiate an immune response. Among intracellular PRRs, Nod-Like Receptors (NLRs), also called Nucleotide Binding leucine-rich Repeats, are widespread in plants, animals, and bacteria. NLRs have also been characterized in fungi, but their role in fungal immunity is not fully established. It has only been shown that some fungal NLRs are implied in conspecific non-self recognition, i.e. the ability for an organism to discriminate its own cells from those of another individual of the same species. This is the case for several NLRs of Neurospora crassa and Podospora anserina, two species belonging to the Sordariales order. Sordariales are among the most common saprophilous, lignicolous, herbicolous and coprophilous fungi and they contribute significantly to carbon storage, nutrient recycling, and plant productivity. Sordariales also encompasses model species such as Neurospora, Podospora and Sordaria, and one of the few groups of thermophilic fungi, the Chaetomiaceae, which plays an important role in the ecology of natural and industrial compost. Morphological and genetic markers have failed so far to give an accurate classification of species within Sordariales. As a consequence, the taxonomic organization of Sordariales families has been highly debated over recent years. By combining population- and comparative genomics, the objective of this thesis is to (1) decipher the evolutionary history of Sordariales, (2) characterize the phylogenetic distribution, domain architecture, composition and size of NLR repertoires in Sordariales and infer the evolutionary changes underlying their variability, and (3) infer the evolutionary forces shaping NLR polymorphism and divergence in Sordariales species.