Le vendredi 15 octobre 2021, Raphaël LEONARD présentera l'examen en vue de l’obtention du grade académique de Docteur en Sciences (Collège de doctorat en Biochimie, biologie moléculaire et cellulaire, bioinformatique et modélisation) sous la direction de Frédéric KERFF et Denis BAURAIN.

Cette épreuve consistera en la défense publique d’une dissertation intitulée :

« Bacterial cell-wall architecture: from automated genome selection to evolution of genes and traits ».

Abstract

My aim is to produce possible scenarios for the bacterial evolution based on the bacterial phylogeny and the bacterial cell-wall. For that, we need a selection of genomes which represent the bacterial diversity and are not redundant. However, there is an overabundance of bacterial genomes and most are redundant, so a solution to remove redundant genomes while conserving the bacterial diversity was needed. Yet, none were available when I began my thesis.

I created a tool to automatically cluster genomes and select the best representative for each cluster. The clustering is based on whole genome  comparison and the selection considers genome quality, annotation richness, completeness level and absence of contamination. We called my tool ToRQuEMaDA (Tool for retrieving queried Eubacteria, metadata and dereplicating assemblies) or TQMD for short. TQMD is optimized to dereplicate at high taxonomic levels (phylum) but remains competitive while compared to other programs which are optimized to dereplicate at low taxonomic levels (species).

Based on a selection of 903 genomes, we computed orthologous groups (OGs) from which we studied the synteny of the division and cell wall (dcw) cluster. Using a smaller selection of genomes, 85, we produced a phylogenomic tree based on the 117 most conserved (and single copy) genes in our selection of bacterial genomes. Using this tree, we reconstructed the dcw cluster using an ancestral gene order reconstruction tool and the last bacterial common ancestor (LBCA) cell wall using Bayesian Inference. From our results, it appears that the LBCA was a monoderm already featuring a peptidoglycan layer. We further studied genes involved with the outer membrane (OM) to validate (or invalidate) our results and did not find decisive clues to reject them.

Lien orbi

Le Jury sera composé de :

M. M. GALLENI (Président), Mme et MM. D. BAURAIN (Co-promoteur), C. BROCHIER-ARMANET (Université Lyon 1), D.P. DEVOS (Universidad Pablo de Olavide), B. JORIS, F. KERFF (Promoteur), P. MEYER (Secrétaire).