Mots-Clés

evolution eukaryogenesis viruses phylogenetics phylogenomics

Description

Viruses can deeply affect their hosts’ biological and evolutionary trajectories through a permanent pressure of selection and frequent horizontal transfers of genes of viral or cellular origin. At the scale of deep evolutionary times, these transfers could have had tremendous impacts on the diversification and evolution of their hosts. This is notably true for eukaryotes. Their emergence and early evolution are challenging biological questions, with modern eukaryotic cells characterized by many complex and unique features (nucleus, mitochondria, mitosis and more) that are thought to have already been present in LECA, the Last Eukaryotic Common Ancestor. Over the years, several scenarios have been proposed regarding eukaryogenesis, but the roles viruses could have played remain largely underexplored.

However, viruses, and in particular double-stranded DNA viruses from the Nucleocytoviricota phylum (and related), could be significantly involved in the formation of the eukaryotic cell. These viruses are widespread and collectively infect the entire eukaryotic domain. They are involved in massive gene transfers with their hosts (Irwin et al. 2022 Nat Microbiol), culminating to around 10% of the gene content of different green algae (Moniruzzaman et al. 2020 Nature). Importantly, their ancestors were presumably already interacting with proto-eukaryotes, the cellular lineage, regardless of its nature (archaea or other), that accumulated the eukaryotic specific features. We have already identified ancestral transfers of genes oriented cell-to-virus, but also virus-to-cell, likely predating LECA (Guglielmini et al. 2019 PNAS; Kijima et al. 2021 Front Microbiol; Da Cunha et al. 2022 MBE; Guglielmini et al. 2022 Virus Evol).

Project

The VirEukaGen project (ANR-23-CE02-0025) aims to quantitatively and qualitatively assess the roles viruses, especially Nucleocytoviruses and related ones, have played in the origin and early evolution of modern eukaryotes. Through comparative phylogenomic and phylogenetic analyses, we will investigate the respective evolutionary trees of eukaryotes and viruses. The identification of close and remote homologs, through sequence similarity, profile clustering methods and structural predictions, will allow us to explore the long co-evolution between eukaryotes and their dsDNA viruses. We will leverage large resources of reference and environmental eukaryotic and viral genomes, including plankton eukaryotes (Delmont et al. 2022 Cell Genomics) and marine dsDNA viruses (Gaïa et al. 2023 Nature) we lately published.

In this framework, we are looking for an enthusiastic candidate to be recruited for a 2-year-long postdoctorate. The candidate will be involved in all steps of the project, including the effort to develop our genomic resource, notably from recently sequenced oceanic metagenomes.

Applicant’s profile

• PhD in biology (genomics, bioinformatics, evolution, or related)

• Bioinformatics skills (phylogenomics, phylogenetics, large datasets manipulation)

• Knowledge in evolution and genomics of eukaryotes and/or viruses appreciated

• Previous experience in deep evolution appreciated

About us

The successful candidate will join the Eukaryotic Genomic Analyses Laboratory (LAGE; Laboratoire d’Analyses Génomiques des Eucaryotes), a team of around 20 researchers, engineers and students specialized in the structure, ecology and evolution of environmental genomes and communities of eukaryotes and their viruses, using mainly computational approaches. In particular, the team has extensive expertise in omics data to explore the functional characteristics of organisms, their relationships with their environment and the evolution in time and space of genomes, functions, and communities. The LAGE is a member of the Tara consortium (https://fondationtaraocean.org/en/home).

The LAGE is a research team of the Genoscope, a major player in genomics in France, particularly in the development of massive DNA sequencing and bioinformatic analysis techniques. It is located at Evry, 30km south of Paris. It is part of the Fundamental Research Department of the CEA, one of the largest research institutions in France.