A large fraction of diversity of the Archaea is still poorly explored. We are targeting environmental samples to extract genomic data of archaeal lineages of specific interest from an evolutionary point of view. We will probe available sequence data from public environmental metagenomics databases to identify specific lineages. In parallel, we will produce our own data from selected environmental samples containing these lineages. These data will allow filling up poorly explored branches of the tree of Archaea and bring important information on the metabolic diversity and adaptation to various environmental conditions, including the human microbiome.  

Paleo(meta)genomics is an emerging and rapidly growing field where most is yet to be done. In most cases, it consists in the analysis of ancient DNA high-throughput sequencing data obtained from archaeological material or historical samples, and the goal is to retrieve and interpret the genomic information from species that from the past (microbial, eukaryotic, etc.) It combines tools borrowed from different fields, such as genomics, computational biology, microbial ecology, phylogenetics, population genetics, etc. However, at the moment there are no well-established tools for the analysis of this type of data. Hence, each lab must develop custom solutions, combining existing tools or developing new ones to meet the goals of their research programs. As a recently established lab, the microbial paleogenomics unit will spend the upcoming months setting up diverse pipelines and analysis tools for the different projects that will be developed in the coming years, many of which have been already used but need to be re-written in an understandable languaje and structure.

New mouse genetic reference populations obtained from 8 distinct founder strains, including 3 wild-derived strains, have been developped since the 2000s and are now available. These populations captured around 95% of the existing murine genetic diversity and constitute a better model than standard inbred laboratory mouse strains. These populations constitute tools to identify new phenotypes and to map the causative genetic variants (QTL mapping) behind these phenotypes. These populations include : i) Collaborative Cross (CC) inbred strains; ii) Recombinant inbred between CCs (CC-RIXs) and iii) Diversity Outbred. These populations are specifically used in the Mouse Genetics Laboratory to identify new variants involved in host susceptiblity differences to pathogens.