Thomas Badet

Research focus

Modern agricultural practices rely on the extensive use of fungicides for disease control. If fungicides are an effective measure against pathogens when first introduced, history has told us that their efficiency rapidly decreases as resistant individuals emerge in field populations (Fisher et al., 2018; Lucas et al., 2015). Identifying new molecules that are resilient to the evolving populations of the pathogen is therefore crucial for the development of sustainable control strategies. A developing project aims at combining transcriptomics with genome-scale metabolic network modelling and comparative genomics to identify the mechanisms that promote fungicide resistance in an important pathogen of wheat.

Genome diversity is of particular importance in the context of plant-pathogen interactions. Moving away from the "single reference genome" paradigm is a prerequisit for better understading what drives pathogen's evolution in the context of crop production. Indeed, the gene content of a species largely governs its ecological interactions and adaptive potential. A species is therefore defined by both core genes shared between all individuals and accessory genes segregating presence-absence variation. Part of my research focus on accessing the extent of plant pathogens intraspecific genomic diversity through the construction of pangenomes.

In fungal pathogens, transposable elements often constitute a large fraction of the genome. Due to their ability to jump across different positions along the host genome, transposons are major contributors to genome evolution by creating a broad source of genomic variation (Wells and Feschotte, 2020). Ongoing work with Prof. Daniel Croll aims at retracing the evolution of single elements over short time scales using a fungal species as a model.


Short CV

2021-Today > Lecturer part of the laboratory of Prof. Vermeer (University of Neuchâtel, Switzerland)

2018-Today > Scientific Collaborator part of the laboratory of 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)


Publications (Google scholar link)


A systematic screen for co-option of transposable elements across the fungal kingdom
U Oggenfuss, T Badet, D Croll
Mobile DNA 15, 2 (2024)


Recent reactivation of a pathogenicity-associated transposable element is associated with major chromosomal rearrangements in a fungal wheat pathogen
T Badet, SM Tralamazza, A Feurtey, D Croll
Nucleic Acids Research, (2023)


Rapid sequence evolution driven by transposable elements at a virulence locus in a fungal wheat pathogen
NK Singh, T Badet, L Abraham, D Croll
BMC genomics 22 (1), 1-16 (2021)

A population-level invasion by transposable elements triggers genome expansion in a fungal pathogen
U Oggenfuss, T Badet, T Wicker, FE Hartmann, NK Singh, L Abraham, et al,
Elife 10, e69249 (2021)

Machine-learning predicts genomic determinants of meiosis-driven structural variation in a eukaryotic pathogen
T Badet, S Fouché, FE Hartmann, M Zala, D Croll
Nature communications 12 (1), 1-14 (2021)

Emergence and diversification of a highly invasive chestnut pathogen lineage across southeastern Europe
L Stauber, T Badet, A Feurtey, S Prospero, D Croll
Elife 10 (2021)


A 19-isolate reference-quality global pangenome for the fungal wheat pathogen Zymoseptoria tritici
T Badet, U Oggenfuss, L Abraham, BA McDonald, D Croll
BMC biology 18 (1), 1-18 (2020)

The rise and fall of genes: origins and functions of plant pathogen pangenomes
T Badet, D Croll
Current opinion in plant biology 56, 65-73 (2020)

Stress-driven transposable element de-repression dynamics and virulence evolution in a fungal pathogen
S Fouché, T Badet, U Oggenfuss, C Plissonneau, CS Francisco, D Croll
Molecular Biology and Evolution 37 (1), 221-239 (2020)


Expression polymorphism at the ARPC4 locus links the actin cytoskeleton with quantitative disease resistance to Sclerotinia sclerotiorum in Arabidopsis thaliana
T Badet, O Léger, M Barascud, D Voisin, P Sadon, R Vincent, A Le Ru, et al,
New Phytologist 222 (1), 480-496 (2019)


Parallel evolution of the POQR prolyl oligo peptidase gene conferring plant quantitative disease resistance
T Badet, D Voisin, M Mbengue, M Barascud, J Sucher, P Sadon, et al,
PLoS genetics 13 (12), e1007143 (2017)

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


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


Common protein sequence signatures associate with Sclerotinia borealis lifestyle and secretion in fungal pathogens of the Sclerotiniaceae
T Badet, R Peyraud, S Raffaele
Frontiers in plant science 6, 776 (2015)


Resistance to phytopathogens e tutti quanti: placing plant quantitative disease resistance on the map
F Roux, D Voisin, T Badet, C Balagué, X Barlet, C Huard‐Chauveau, et al,
Molecular plant pathology 15 (5), 427 (2014)

Thomas Badet

Maître Assistant (Lecturer)

Bureau A313


University of Neuchâtel
Rue Emile-Argand 11 | CH-2000 Neuchâtel | Switzerland
+41 (0) 32 718 22 05 | thomas.badet@unine.ch