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Genome dynamics and DNA repair in the bdelloid rotifer Adineta vaga

par Houtain, Antoine
Président du jury Dennis, Alice AD
Promoteur Van Doninck, Karine
Co-Promoteur Flot, Jean-François
Publication Non publié, 2024-05-17

Thèse de doctorat

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Résumé :

Sexual reproduction and DNA repair mechanisms are processes that shape the evolution of eukaryotic species’ genomes. There appears to be a paradox in sexual reproduction because it has no evident direct benefits while it is almost universal among eukaryotes. DNA repair mechanisms are also crucial for reproduction as they ensure genome integrity across generations while simultaneously generating errors, thereby fostering genetic diversity.Understanding how these processes shape genetic diversity and genomes is of significant interest in biology. One approach to gain insights into their evolutionary impact is by studying species with alternative modes of reproduction while showing a high tolerance to DNA damage.One of the most notorious animal model system, reproducing asexually through a modified meiosis and exhibiting exceptional resilience to DNA-damaging conditions like desiccation and radiation, is the bdelloid rotifer species Adineta vaga, which is the primary focus of this PhD. More specifically, this PhD research investigates the genome dynamics, DNA repair mechanisms, and the consequences of asexual reproduction on genetic diversity in Adineta vaga.The work presented in this thesis begins by comparing genome assembly methods to prevent haplotig contamination in haploid assemblies, as well as obtaining chromosome-scale assemblies to study the genome evolution of A. vaga. Subsequently, using the best strategies we determined, it describes the genome structure of A. vaga, providing evidence for pairs of homologous chromosomes and recombination. Furthermore, it unveils the first description of a trans-generational DNA repair mechanism in an animal species, providing new insights onA. vaga's survival mechanisms in harsh environmental conditions. The thesis also explores how long-term asexuality, coupled with intra-individual homologous recombination, impacts the transposable element dynamics, the genome heterozygosity, and allele-specific expression. Lastly, this thesis presents preliminary results on the population genomics in Adineta spp., along with the intriguing possibility of programmed DNA elimination in Adineta spp.