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Habilitation à diriger des recherches

Genome evolution and adaptations to plant parasitism in nematodes

Abstract : Nematodes are non-segmented roundworms, mostly transparent and less than 1 mm long. Although nearly invisible, they are one of the most species-rich groups of animals. The majority of nematodes are free-living and feed on bacteria and fungi, but the most notorious species are animal and plant parasites. Plant-parasitic nematodes cause approximately 100 billion Euros in damages to the world agriculture every year. Plant parasitism has appeared at least 4 times independently during the evolutionary history of nematodes. Morphological similarities have emerged in a convergent manner in these parasites and specific genomic singularities might be associated as well. The first genome for a plant-parasitic nematode, the root-knot nematode Meloidogyne incognita was sequenced and annotated in 2008 as part of an international consortium coordinated by our team. Comparisons with the genomes of other nematodes were made possible and revealed idiosyncrasies that might be linked to plant parasitism. A major part of my research consists in identifying such idiosyncrasies in nematode genomes that could be related to adaptations to plant parasitism. I have shown that nematodes acquired, via lateral gene transfers, a plethora of genes of bacterial and fungal origins involved in successful parasitic interactions with plants (effectors). These evolutionary events, considered as rare in animals, have apparently played an important role in adaptation to plant parasitism. Large scale comparisons of the genomes of plant parasites with those of other eukaryotes allowed us to identify a set of genes absent from non parasitic species. This specificity to parasites suggests that the genes could be involved in plant parasitism. We have shown that, indeed, silencing of these genes significantly reduced the parasitic success of root-knot nematodes. Because they are absent from other species, these genes constitute interesting targets for the development of new and more specific control methods against phyto-nematodes. Another singularity of the Meloidogyne incognita genome resides in its structure itself. Indeed, the genome is mainly present in pairs of copies similar yet divergent at the nucleotide level. This singular structure might be related to the M. incognita peculiar reproductive mode. This root-knot nematode reproduces asexually and without meiosis. We suppose that in the absence of sexual reproduction, the equivalents of homologous chromosomes found in sexual species are free to diverge substantially. Sexual reproduction is considered as an evolutionary dead end in animals. Nevertheless, M. incognita is able to infest more plants than its sexual cousins and possesses a larger geographic distribution. Furthermore, it is able to overcome plant resistance and thus adapt to changes. Presence of a proportion of genes in divergent copies might constitute a pool for plasticity. Evolution capabilities in animals lacking sexual reproduction, in particular plant pests, is a topic that I will try to develop in the next few years.
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Etienne Danchin. Genome evolution and adaptations to plant parasitism in nematodes. Life Sciences [q-bio]. Université Nice Sophia Antipolis, 2014. ⟨tel-02801776⟩

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