PPU2014-39 PhD PROPOSAL FOR THE PASTEUR-PARIS UNIVERSITY INTERNATIONAL PROGRAM

Deadline for full application: December 15th, 2013

Interviews: March, 2014

Start of the Ph.D.: October 1st, 2014

 

 

Department: Microbiology

Title of the PhD project: Phylogenomics and the Tree of Life: digging up the deep evolutionary history that shaped modern microbial biodiversity.

Name of the lab: BMGE

Head of the lab: Patrick Forterre

PhD advisor: Simonetta Gribaldo

Email address: simonetta.gribaldo@pasteur.fr

Web site address of the lab: http://www.pasteur.fr/ip/easysite/pasteur/fr/recherche/departements-scientifiques/microbiologie/unites-et-groupes/unite-de-biologie-moleculaire-du-gene-chez-les-extremophiles/les-membres-de-l-equipe/simonetta-gribaldo

Doctoral school affiliation and University: Complexité du Vivant (CdV), University Pierre et Marie Curie (Paris 6)

 

Presentation of the laboratory and its research topics:

Within the Unit BMGE Simonetta Gribaldo runs the independent group “Microbial Phylogenomics”. Research focuses on major evolutionary questions along the Tree of Life (Bacteria, Archaea, Eukaryotes) through phylogenomics approaches. In particular, we seek to reconstruct the phylogeny of each domain, infer the nature of their ancestors, highlight macro-evolutionary patterns along their diversification, and dissect their evolutionary relationships.

Over the past few years, we have contributed original research on various subjects related to large-scale microbial evolution and the Tree of Life. Building on the growing number of archaeal complete genomes, we have established the first robust reference trees for the whole domain Archaea based on analysis of a large number of markers alternative to 16S rRNA (1, 5, 10). This solid phylogeny now constitutes an essential frame to fully understand the evolution of this important fraction of microbial diversity. We are deeply interested in the debated evolutionary relationships between Archaea and Eukaryotes (6). Concerning Bacteria, we work to clarify the phylogeny and diversity of major phyla and their role in key events in the history of eukaryotes (2, 3, 8). We also seek to infer the nature of the last common ancestor of Eukaryotes and the early evolution of this domain (4, 7). Finally, we investigate the timing of emergence of major metabolic capabilities, which can inform on the nature of the earliest microbiota and of the conditions of early Earth (9).

Current research subjects in the lab continue to explore the phylogeny of the three Domains of Life, their evolutionary relationships, and the history of major cellular processes. 

Both French and English are spoken in the group.

 

Description of the project:

(1 page, Arial font size 11 : 600 words in total with at least 50% dedicated specifically to the proposed PhD project(s))

 

Yet, the processes that have led to such diversity over more than 3 billion years of evolution remain largely unknown.

Phylogenomics is a relatively recent discipline emerged with the genomic era. It consists in exhaustive in silico surveys of the taxonomic distribution, genomic context, and phylogenetic analysis of the components of a given biological system (biochemical pathway, cellular structure, macromolecular assembly, …). This allows the reconstruction of accurate evolutionary scenarios of key life processes in terms of horizontal gene transfers, gene family expansions, gene losses, functional adaptation or modification, etc. Combined with the growing availability of functional and ‘omics’ data from a large fraction of microbial diversity, such kinds of analyses are greatly expanding our understanding of the evolutionary processes shaping microbial cellular system.

 

 

Various subjects may be proposed according to the candidate’s experience and preferences:

Origin and early evolution of Eukaryotes: continue dissecting the genetic makeup of the eukaryotic ancestor through the phylogenomic study of key cellular processes, either specific, or having common ancestry with bacteria or archaea. Try resolving the evolutionary relationships among the major eukaryotic lineages. 

Phylogeny of Bacteria: carry out a global evolutionary analysis of a major bacterial phylum, find reliable multiple markers to build a robust reference tree, characterize the gene content of its ancestor and subsequent evolution in terms of gene losses, gene family expansions, horizontal gene transfers. Dissect the evolutionary history of specific cellular processes.

Diversity of the Archaea: make use of the solid reference tree obtained in the lab to perform large-scale comparative genomics analyses to highlight macro-evolutionary patterns in relation to specific life trait adaptations.

Connections among the three domains of life: exhaustive investigation of horizontal gene transfers among eukaryotes and prokaryotes, in both directions. How many and what genes are transferred, what are the lineages most often involved, and what are the possible mechanisms. 

Early metabolisms and the first steps of modern life: origin and evolutionary history of major biogeochemical cycles, impact of rise in oxygen on cellular processes, timing of emergence of oxygenic and anoxygenic photosynthesis. 

During his/her PhD, the student will acquire important principles of early microbial evolution and the methodological basis of phylogenomics, both important tools of modern microbiology.

 

Some relevant publications of the lab:

1) Borrel G, O'Toole PW, Harris HM, Peyret P, Brugère JF, Gribaldo S. (2013) Phylogenomic data support a seventh order of methylotrophic methanogens and provide insights into the evolution of methanogenesis. Genome Biol Evol [Epub ahead of print]

2) Raymann K, Bobay LM, Doak TG, Lynch M, Gribaldo S. (2013) A genomic survey of Reb homologs suggests widespread occurrence of R-bodies in proteobacteria. G3 (Bethesda) (3):505-16.

3) Criscuolo A and Gribaldo S. (2011) Large-scale phylogenomic analyses indicate a deep origin of primary plastids within Cyanobacteria. Mol Biol Evol 28(11): 3019-32.

4) Desmond E, Brochier-Armanet C, Forterre, Gribaldo S. (2011) On the last common ancestor and early evolution of eukaryotes: reconstructing the history of mitochondrial ribosomes. Res Microbiol 162(1):53-70. 

5) Brochier-Armanet C, Forterre P, Gribaldo S. (2011) Phylogeny and evolution of the Archaea: one hundred genomes later. Curr Op Microbiol 14(3):274-81.

6) Gribaldo S, Poole AM, Daubin V, Forterre P, Brochier-Armanet C (2010) The origin of eukaryotes and their relationship with the Archaea: are we at a phylogenomic impasse? Nat Rev Microbiol  8(10): 743-52.

7) Desmond E and Gribaldo S. (2009) Phylogenomics of sterol synthesis: insights into the origin, evolution and diversity of a key eukaryotic feature. Genome Biol Evol 2009: 364-81.

8) Emiliani G, Fondi M, Fani R, Gribaldo S. 2009 A horizontal gene transfer at the origin of phenylpropanoid metabolism: a key adaptation of plants to land. Biol Direct. 4:7.

9) Gribaldo S, Talla E, Brochier-Armanet C. 2009 Evolution of the haem copper oxidases superfamily: a rooting tale. Trends Biochem Sci. 34(8):375-81.

10) Brochier-Armanet C, Boussau B, Gribaldo S, Forterre P. (2008) Mesophilic Crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota. Nat Rev Microbiol 6(3): 245-52.

 

Keywords:

Evolution, Phylogenomics, Tree of Life, Horizontal Gene Transfer. 

 

Expected profile of the candidate (optional):

The ideal candidate has a strong interest in microbial evolution, and ideally previous experience with sequence analysis. Some programming skills or a real desire to learn them will be a plus. 

 

Contact:

simonetta.gribaldo@pasteur.fr

 

Mis à jour le 12/11/2013