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Évolution des génomes et modes de reproduction de Cryphonectria parasitica, l'agent causal du chancre du châtaignier, dans le contexte d'une double introduction en Europe.

Abstract : Biological invasions are a major component of global change, causing many disruptions in ecosystem functioning and human activities. Their frequency has been increasing since the end of the 20th century, particularly in the case of forest pathogenic fungi. In this introduction context, the adaptation of pathogens to new environments and hosts is an evolutionary paradox, due to the low genetic diversity generally introduced. Evolutionary mechanisms allowing the adaptation of these organisms have been proposed, but with the exception of a few model species, often pathogenic agents of crops plants, these mechanisms remain poorly studied in fungi.The purpose of this thesis is to study the evolution of Cryphonectria parasitica populations, the causal agent of chestnut blight, in the context of a dual introduction into Europe. Native of Asia, it was introduced into North America at the end of the 19th century and almost caused the extinction of the American chestnut. It was then introduced into Europe from these North American and Asian populations at the beginning of the 20th century. In Europe, populations are mainly structured in clonal lineages, unlike the original populations. This suggests a change in reproductive mode that may be involved in the invasive success of these populations. However, previous studies have shown that several genotypes not belonging to the main clonal lineages have been maintained during colonization and that crosses between these clonal lineages exist, even if they seem to be limited. The objectives of this thesis were to better describe crosses between clonal lineages and to identify possible barriers to crosses between them.In a first part, the genome of 50 French, North American and Asian isolates confirmed the strong similarity of isolates belonging to the same European clonal lineage, with the exception of small divergent regions exchanged between these genomes, more frequently observed between introduced lineages from the same origin. In addition, 5 of the 6 lineages studied carry a signature of recent recombination of the region carrying the mating type locus. This gives the clonal lineages the ability to self-fertilize (haploid-selfing). These results underline that the maintenance of clonal lineages in a heterothallic fungus such as C. parasitica (i.e. crosses involve genotypes with different sexual types) does not always and solely involve asexual reproduction.In a second part, the assembly of genomes of isolates from the native and introduced areas, using long-read sequencing methods, made it possible to compare their structure and chromosome composition, and to identify possible barriers to recombination. However, no major rearrangements were detected, except for a region of 1Mb adjacent to the sexual locus, which is very rich in transposable elements and variable between genomes. These results seem to refute the hypothesis of reproductive isolation by chromosomal rearrangement. On the other hand, areas containing many transposable elements could allow a rapid evolution of C. parasitica genomes during introduction.A final part deals with the study of genotypes that appear to originate from crosses between the main clonal lineages in order to explore the recombination processes between the gene pools of the two introductions and to identify possible barriers to hybridization, potentially associated with unfavorable genetic combinations.This work underlines the contribution of genomic data to the understanding of recombination processes and the detection of genetic variations in an invasive pathogenic fungus affecting its evolutionary capacities.
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Arthur Demené. Évolution des génomes et modes de reproduction de Cryphonectria parasitica, l'agent causal du chancre du châtaignier, dans le contexte d'une double introduction en Europe.. Biodiversité et Ecologie. Université de Bordeaux, 2019. Français. ⟨NNT : 2019BORD0428⟩. ⟨tel-03448853⟩

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