Genetic and ecological insights of Swiss morels ("Morchella" spp.), including an agricultural perspective

True morels (Ascomycota, Pezizomycetes, Morchella) are one of the rare edible mushrooms that can be collected in the wild and cultivated at commercial scales. The morel fruiting body is a healthy food appreciated worldwide as gourmet food and for its medicinal properties. Morchella have a complex taxonomy but are basically divided into three main clades (Rufobrunnea, Esculenta, Elata). Morchella also display a complicated lifecycle and trophic system, that remain partially unknown. Morels can reproduce asexually, and sexually by producing ascospores-bearing fruiting bodies. The mating type locus is the master regulator of sexual reproduction, and the genes it contains inform on the reproductive system of an organism. In Morchella, homothallism, pseudohomothallism, and heterothallism exist. Morels were domesticated in the early eighties, and since then the cultivation process has not stopped to improve. China is currently the only country to commercialize cultivated morels at large scale. In Switzerland, markets are provided with environmentally unsustainable and potentially socially unfair morel mushrooms. Harvesting morels in the wild cannot meet the demand, hence the development of cultivation in the Switzerland is needed. A native strain must be domesticated, because importing non-indigenous cultivars can cause biodiversity threats, namely invasiveness and hybridization. To do so, it is crucial to study Swiss morels. This thesis provides the first knowledge background necessary to develop morel cultivation in Switzerland. In section 2, the biodiversity of Morchella was assessed in nine cantons of the country. In this survey one species of the Esculenta clade (Morchella esculenta) and three described species of the Elata clade (Morchella importuna, Morchella deliciosa/Mel-13, Morchella pulchella species complex) were found. In addition, four new lineages were discovered, one of which was described as a new species (Morchella helvetica sp. nov.) in section 3. Section 4 evaluated an AI-based identification tool (the Centroid-based approach) that was able to identify 83% of the morel species based on genetic sequences of the internal transcribed spacer. The performance was comparable with four-locus phylogenetic analyses that were able to identify 84% of the Morchella at species level. In sections 5-6, the sexual reproduction system of Swiss Morchella was investigated. The reliability of four primer pairs was tested, the mating genotype of single-ascospore isolates of Swiss strains was assessed, and the genetic structure of the mating type locus was determined analyzing two whole genomes that were sequenced for this purpose. This revealed that Swiss morels were mainly heterothallic. The last sections investigated biologic interactions between Morchella and other organisms that it could encounter in soil. In section 7, tripartite interactions between Morchella, the bacterium Pseudomonas koreensis, and a bacteriophagous amoeba Acanthamoeba castellanii were investigated. This revealed an unexpected association between the fungus and the amoeba to thrive in the presence of the bacterium. In addition, it was demonstrated for the first time that P. koreensis can form biofilm around Morchella hyphae, and that amoeba can use hypha to facilitate their movement across unsaturated areas of the medium (i.e., fungal highways). Finally, in section 8, the mycophagous nematode Aphelenchus avenae and three fungal contaminants isolated from a fruiting body cultivation assay (Penicillium sp., Cephalotrichum sp., Aspergillus westerdijkiae). Overall, Morchella had a natural resistance against the predatory nematodes and outcompeted the fungal contaminants.