Doctoral thesis (Dissertations and theses)
Bacterial cell-wall architecture: from automated genome selection to evolution of genes and traits.
Léonard, Raphaël
2021
 

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Keywords :
cell wall; Bacteria; Phylogenomics; dereplication; Prokaryotes; dcw cluster; torquemada; TQMD
Abstract :
[en] 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.
Research Center/Unit :
CIP - Centre d'Ingénierie des Protéines - ULiège
Biological Sciences from Molecules to Systems - inBioS
Disciplines :
Microbiology
Genetics & genetic processes
Biochemistry, biophysics & molecular biology
Author, co-author :
Léonard, Raphaël  ;  Université de Liège - ULiège > InBioS
Language :
English
Title :
Bacterial cell-wall architecture: from automated genome selection to evolution of genes and traits.
Defense date :
2021
Number of pages :
190
Institution :
ULiège - Université de Liège
Degree :
Docteur en sciences
Promotor :
Kerff, Frédéric  ;  Université de Liège - ULiège > Integrative Biological Sciences (InBioS)
Baurain, Denis  ;  Université de Liège - ULiège > Integrative Biological Sciences (InBioS)
President :
Galleni, Moreno ;  Université de Liège - ULiège > Integrative Biological Sciences (InBioS)
Secretary :
Meyer, Patrick  ;  Université de Liège - ULiège > Integrative Biological Sciences (InBioS)
Jury member :
Joris, Bernard ;  Université de Liège - ULiège > Département des sciences de la vie
Brochier-Armanet, Céline
Devos, Damien
Funders :
FRIA - Fonds pour la Formation à la Recherche dans l'Industrie et dans l'Agriculture [BE]
Available on ORBi :
since 13 September 2021

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