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Genomic analysis of eukaryotes

Genomic analysis of eukaryotes

Published on 8 October 2019
L'analyse génomique eucaryote

Our team's bioinformatics research is oriented toward the comparative analysis of eukaryote genomes. Our genomic approaches to the exploration of new genomes derived from various sequencing projects and annotated by the Genoscope platform target plants, animals, fungi and protozoa.

Part of our activity is centered on research on ancestral whole-genome duplication (WGD) events or other polyploidizations. This type of evolutionary event is considered to be an essential agent in the acquisition of new functional or regulatory capabilities in the emergence of new species. Major evolutionary lines such as teleostean vertebrates or angiosperm plants are very certainly derived from polyploidization.

The sequence of the genome of rape, the leading oil-yielding plant cultivated in Europe, constitutes an excellent example. The plant, a member of the Cruciferae family, like mustard, cabbage and turnip, has accumulated, during its evolution, 72 ancestral genomes resulting from numerous polyploidization cycles and making the genome one of the most highly duplicated among the flowering plants.

Our studies also address characterization, by 'omic' approaches, of the host-parasite relationship in certain phyla. A good example consists of the trypanosomes, parasites that infect animals and plants via insects. In man and animals, trypanosomiasis and leishmaniasis, responsible for serious diseases including sleeping sickness, Chagas' disease and kala-azar, have been the subject of in-depth studies using genomic approaches. The world of plant trypanosomes is vast. Lack of data has hitherto prevented a classification being established. The trypanosomatids found in plants may be responsible for great economic harm and give rise to frequent insecticide treatments, which are expensive and polluting the Amazon basin. Trypanosomes may be markedly different from each other and may thus call for distinct prophylactic measures.  Our team undertook « comparative » sequencing of 2 trypanosome genomes that were at first sight very different. The first trypanosome is present in sick palm trees in South America and is harmful. The second, obtained from healthy euphorbia in the South of France, is harmless. Analysis of their genomes showed, surprisingly, that the majority of their genes were identical with a gene content considerably less than that of the known genomes of trypanosomes that infect animals. Our studies showed that, during their evolution, the 2 trypanosomes retained a minimum set of genes and reduced their metabolic system so as to only retain the most important biological processes. While animal trypanosomes duplicate their genes to form a multitude of copies, the 2 trypanosomes under study only retained 1 copy in most cases. Trypanosome colonization of plants would appear to be easier than colonization of animals. The temperature is stable and nutrients are present continuously. The parasites are thus under less threat and do not require a genome as diversified as that of animal trypanosomes.

The same approach is currently being used on a group of ubiquitous parasitic protists able to infect certain toxic microscopic algae responsible for the blooms known as red tides, Amoebophrya, which are poorly known compared to other marine planktons. Our objective is to identify the molecular components, mechanisms and evolutionary forces which determine the ability of the specialized parasites to infect their primary host and adapt to a new host. In order to so, genomic and transcriptomic analyses are being conducted on 2 strains of Amoebophrya that are distinct in terms of their impact on their hosts. A worldwide impact study of the parasites is to be conducted thanks to collection of the plankton sequences generated by the Tara Oceans project.

A further example of the plant-host relationship derives from fungal genomics, which is another of our interests. Comparative analysis of the genomes of symbiotic fungi reveals the mechanisms used to dialog and interact with the host plant, while demonstrating the extraordinary diversity through which symbiotic fungi interact with their partners using a varied molecular tool kit.

Currently, the study of the dynamics of emergence of genetic novelties in fungi is an important aspect of our research operations with a view to characterization of the 'gene signatures' of certain phylogenetic branches among the Ascomycetes via a genomic approach.