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Déterminants génomiques de la spécialisation à l’hôte chez le champignon phytopathogène polyphage Botrytis cinerea

Abstract : Phytopathogenic fungi are major parasites to wild or domesticated plant species. The grey mold fungus, Botrytis cinerea, infects more than 1400 plant species and thus is considered a broad generalist. However, recent data have revealed population structure correlated to the host of origin of isolates. This observation raises the hypothesis of ongoing host specialization in a generalist species. Studying this question could greatly deepen our theoretical knowledge of the evolutionary mechanisms involved in the early stages of population divergence and subsequent speciation. This thesis aims (i) to formally demonstrate the host specialization in B. cinerea’s populations and determine its magnitude, and (ii) to identify the genomic determinants of this specialization. Thus, I studied population structure based on 683 isolates characterized using microsatellite markers. We compared the inferred genetic structure with variations in aggressiveness measured through cross-pathogenicity tests on multiple hosts. These experiments and analyses confirmed the specialization of B. cinerea to tomato and grapevine hosts. Besides these specialized lineages, the species B. cinerea is composed of generalist individuals capable of infecting multiple hosts. I sequenced the whole genome of 32 individuals and characterized nucleotide polymorphism. Structure inference and genomic genealogy methods allowed us to more accurately define the population structure and identify a lineage specialized on tomato. Lastly, McDonald-Kreitman tests and genomic scans methods allowed the identification of genes under divergent natural selection between populations, revealing possible genomic determinants of specialization. This work can serve as foundation for the validation of multiple genes involved in host-specific pathogenicity of B. cinerea, and pave the way for the implementation of efficient strategies for managing pathogen reservoirs and new agricultural practices for controlling grey mold.
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Alex Mercier. Déterminants génomiques de la spécialisation à l’hôte chez le champignon phytopathogène polyphage Botrytis cinerea. Phytopathologie et phytopharmacie. Université Paris Saclay (COmUE), 2019. Français. ⟨NNT : 2019SACLS442⟩. ⟨tel-02910356⟩

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