Thomas Badet

Evolution of gene expression

My project is embedded in the laboratory’s principal research on the evolutionary mechanisms of fungal pathogenicity using Zymoseptoria tritici as a model species. Effectors are expressed by fungal pathogens to promote disease. The rapid evolutionary processes observed in the effector gene repertoire are tightly linked to the rapid gains in virulence of the pathogen. Most effectors are encoded by highly polymorphic short open reading frames (ORFs) that often share no conserved domains, suggesting a recent origin. In Z. tritici, effectors not only show strong sequence variation but highly variable transcriptional profiles among field isolates. Additionally, effectors often bear the hallmarks of “young genes” and are likely the result of recent de novo gene emergence from non-coding DNA. Although a large number of effector genes likely contribute to the Z. tritici infection process and are major determinants of host range, little is known about effector origins and their transcriptional regulation. The aim of my project is to identify transcriptional variation associated with Z. tritici putative young genes and retrace the regulatory mechanisms that were recruited to create de novo effector genes from non-coding DNA. Identifying the evolutionary origins of effectors and their transcriptional regulation would resolve major questions in virulence evolution of plant pathogens and elucidate fundamental mechanisms of gene formation. 


Short CV

2018- Post-Doc in Pathogen Evolution with Prof. Croll (University of Neuchâtel, Switzerland)

2014-2017 PhD in Plant Pathology with Dr. Raffaele (INRA Toulouse, France)

2012-2014 MSc in Plant Biology (University of Toulouse, France)



Badet, T., Peyraud, R., Mbengue, M., Navaud, O., Derbyshire, M., Oliver, R.P., et al. (2017a). Codon optimization underpins generalist parasitism in fungi. Elife, 6, e22472.

Badet, T., Peyraud, R. & Raffaele, S. (2015). Common protein sequence signatures associate with Sclerotinia borealis lifestyle and secretion in fungal pathogens of the Sclerotiniaceae. Front. Plant Sci., 6, 776.

Badet, T., Voisin, D., Mbengue, M., Barascud, M., Sucher, J., Sadon, P., et al. (2017b). Parallel evolution of the POQR prolyl oligo peptidase gene conferring plant quantitative disease resistance. PLOS Genet., 13, e1007143.

Mbengue, M., Navaud, O., Peyraud, R., Barascud, M., Badet, T., Vincent, R., et al. (2016). Emerging Trends in Molecular Interactions between Plants and the Broad Host Range Fungal Pathogens Botrytis cinerea and Sclerotinia sclerotiorum. Front. Plant Sci., 7, 422.

Roux, F., Voisin, D., Badet, T., Balagué, C., Barlet, X., Huard-Chauveau, C., et al. (2014). Resistance to phytopathogens e tutti quanti: Placing plant quantitative disease resistance on the map. Mol. Plant Pathol., 15, 427–432.

Thomas Badet

Maître assistant



+41 32 718 22 05

Bureau A313