Genome and Transcriptome Analyzes in the Ectomycorrhizal Fungus Paxillus involutus

Mycorrhizal symbioses are formed between plant root systems and compatible fungal hyphae that results in a complex mixed structure. They are found in all ecosystems and with the majority of land plants such as forest trees or crops that are of commercial interest. Mutual exchange of nutrients between the two symbionts is central to the successful functioning of the symbioses. In order to understand the processes involved in the development of this symbiosis and to increase our knowledge in this field of study, I have used new molecular methods emerging from functional genomics, a faster way to link functions to genes. Particularly, I have developed and applied the microarray technology to further characterize this complex type of plant microbe interaction. Using this technique, we can decipher the complex molecular programs that lead to the mycorrhizal symbiosis, survey genome-wide patterns of gene expression within and among species as well as employing the information it contains in quantitative genetics studies. I believe that this new tool will be increasingly used by evolutionary biologists and in molecular ecology studies in the future to address questions such as those presented in this thesis. This thesis presents information on the genome and the transcriptome characteristics of our model mycorrhizal fungus Paxillus invoulus. Its nuclear haploid genome was estimated to be 21.5 Mbp in length and to contain ca 7,700 genes. An Expressed Sequence Tag (EST) project was initiated to obtain sequence information both on the coding genome of the fungus as well as for one of its plant hosts the European birch (Betula pendula). Based on sequencing information of more than 10,000 ESTs, a unique set of 2,284 cDNAs either of fungal or plant origin were selected and amplified. These were spotted onto glass slides. These DNA chips or cDNA microarrays were used to survey the expression of the genes represented on the arrays at distinct developmental stages during formation of the symbiotic tissue. Notably, it revealed that the plant responds to the fungus and the formation of the symbiotic tissue by undergoing a typical hypersensitive response also observed in plants when attacked by various pathogens. Furthermore, this response was completely repressed in the more mature mycorrhizal tissue which probably allows the formation of a functional mycorrhizal association to occur. Finally, we use these cDNA microarrays to compare the transcriptome and the genome of isolates presenting phenotypic variations or of different origin. We found that the genome of P. involutus is plastic and contains a high number of divergent genes and / or genes that vary in copy number. Furthermore, transcript profiling in strains presenting different abilities to develop the symbiotic tissue also allowed the characterization of genes related to the symbiosis which show variability due to changes in the promoter elements and levels of transcription factors rather than gene copy number alterations