We are looking for an enthusiastic Ph.D student to work on pangenomes of Archaea. See below a description of the project.
A characteristic of natural populations is that they are comprised of individuals that are, in the majority of cases, not genetically identical to each other. In the microbial world, variation between individuals appears both as divergence at the single nucleotide level and the presence of hypervariable genomic islands within a more stable set of genes shared by multiple individuals. The total pool of genetic material comprised by all members of a species is referred to as the ‘pangenome’ [1, 2]. It consists of the core/persistent genome that is common to almost all members of a species, plus all the flexible/variable genome content that is present in some members of the species.
Genome-resolved metagenomics, in which shotgun sequencing of environmental DNA is assembled and binned into draft genomes, has profoundly reshaped our understanding of the distribution, functionalities and roles of Archaea. Within the domain, major supergroups are Euryarchaeota, which includes many methanogens, the TACK, which includes Thaumarchaeaota that impact ammonia oxidation in soils and the ocean, the Asgard, which includes lineages inferred to be ancestral to eukaryotes, and the DPANN, a group of mostly symbiotic small-celled archaea. These archaea are not restricted to extreme habitats, but are widely distributed in diverse ecosystems [3–5].
However, there has been only limited analysis of the extent of heterogeneity in gene content within archaeal species [6, 7]. The wealth of metagenome-assembled genomes (MAGs) allows access to gene content heterogeneity within environmental populations of uncultivated archaea. In fact, 34 species-level groups of Archaea, as defined by the Genome Taxonomy DataBase , contain more than 10 distinct genomes, a number that has been shown to be sufficient to define pangenomes and detect genomic islands using the tools PPanGGOLiN and panRGP we recently developed in our lab [9, 10].
The aim of this PhD thesis is to leverage the hundred thousand MAGs available using our recent methodological developments for the comparative study of meta-pangenomes in Archaea. First, we propose to systematically analyze the pangenomes of archaeal species. Particular attention will be given to the functional analysis of the genomic islands with regard to the biological capacities of organisms in terms of defense systems and metabolic processes. The description of pangenomes from several archaeal species will then allow inter-pangenome comparisons and, thus, the exploration of the dynamic of the genomic islands between different species of Archaea. The future discoveries will benefit further functional characterization by biochemists of our institute. The second part of the PhD project will consist in a meta-pangenomic approach to track the spatio-temporal distribution and abundance of genomes that belong to the same species using read recruitment from metagenomic projects . We plan to add available physical and chemical parameters from sampling sites and perform correlation analysis between the environmental parameters and the genome abundances. The most interesting species to investigate will be partly selected based on their metabolic capacities we will define in the first aim of the project. We anticipate this will yield unique insights into the functional basis of microbial niche partitioning and fitness of archaeal species.
For more information, you may contact Raphaël Méheust (firstname.lastname@example.org) and David Vallenet (email@example.com). The position will be located at the Genoscope in Evry.
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