A pioneering exploration of the intraspecific genomic landscape of adaptation in non-vascular plants : the case of the liverwort Marchantia polymorpha ; Première exploration du paysage génomique intraspécifique de l'adaptation chez les plantes non vasculaires : le cas de l'hépatique Marchantia polymorpha

Plant adaptation to a terrestrial life 500 million years ago played a major role in the evolution of life on Earth. Plants still play a crucial role at present time, as bases of most ecosystems, and consequently base of all human civilizations. Understanding their adaptation to past and present modification of their living conditions is a key to understand the past and be able to respond to future agricultural challenges. Plants sciences made great advances in understanding plant response to their environment, but most studies focused on the angiosperm lineage which contains crops. Nevertheless, to get a broader picture of land plant (Embryophytes) adaptation to various conditions, in the framework of 500 million years of evolution on land, it is essential to study other land plant lineages. In line with this logic, this work will focus on the non-vascular plant model Marchantia polymorpha, whose lineage diverged from vascular plants around 480 million years ago. We developed an intraspecific diversity dataset that allowed us to uncover some mechanisms of adaptation in M. polymorpha. Analyses of selection signatures on genes enabled us to distinguish conserved functions under strong purifying selection from variable ones undergoing balancing selection or selective sweeps. Using this intraspecific diversity dataset, genome-wide associations studies (GWAS) could be performed on the response of M. polymorpha to climatic conditions but also to the fungal pathogen Colletotrichum nymphaeae (biotic stress). Finally, a gene-based pangenome was built and allowed identifying genes with a presence-absence variation between accessions, that are often associated with stress response and local adaptation. Crossing these three approaches, we found gene families that seem involved in M. polymorpha response to stresses. Among them can be cited the terpene synthases, the peroxidases, the NBS-LRR (NLR), the lectins, the lipoxygenases or the polyphenol oxidases. Most of these functions are shared with other land plants, showing ...