Evolutionary genomics of plant-pathogen interactions

Most plants face attacks by fungal pathogens. In agriculture, outbreaks of diseases are frequent and pose a significant threat to sustainable food production. What enables pathogens to overcome host defenses and cause damage is poorly understood. A key evolutionary step for pathogens is to evolve effectors that specifically target and disable the plant immune system.

Our group uses experimental and population genomics tools to analyze the rapid emergence of pathogens. A major focus is to use genome-wide association studies (GWAS) to directly identify the genes in pathogen genomes linked to the breakdown of host resistance. We also assemble complete genomes to analyze mechanisms that generate high degrees of sequence polymorphism. We are particularly interested in the action of transposable elements (selfish elements in the genome) and the evolution of gene regulation. Our group also conducts population genomic studies to analyze the process of adaptive evolution in natural field populations.


Recent Pubications

  • Comparative Genomics of Smut Pathogens: Insights From Orphans and Positively Selected Genes Into Host Specialization
    Benevenuto, J; Teixeira-Silva, NS; Kuramae, EE; Croll, D; Monteiro-Vitorello, CB
    FRONTIERS IN MICROBIOLOGY, 9 https://doi.org/10.3389/fmicb.2018.00660 APR 6 2018
  • Genome-wide evidence for divergent selection between populations of a major agricultural pathogen Molecular Ecology
    Fanny E Hartmann; Bruce A McDonald, Daniel Croll
    Molecular Ecology, https://doi.org/10.1111/mec.14711  May 2018
  • Population genomics analyses of European ibex species show lower diversity and higher inbreeding in reintroduced populations 
    Grossen, Christine; Biebach, Iris; Angelone-Alasaad, Samer; et al. 
    EVOLUTIONARY APPLICATIONS, 11 (2): 123-139  https://doi.org/10.1111/eva.12490   FEB 2018 
  • Acetate provokes mitochondrial stress and cell death in Ustilago maydis 
    Kretschmer, Matthias; Lambie, Scott; Croll, Daniel; et al. 
    MOLECULAR MICROBIOLOGY, 107 (4): 488-507 https://doi.org/10.1111/mmi.13894 FEB 2018
  • Pangenome analyses of the wheat pathogen Zymoseptoria tritici reveal the structural basis of a highly plastic eukaryotic genome 
    Plissonneau, Clemence; Hartmann, Fanny E.; Croll, Daniel 
    BMC BIOLOGY, 16: https://doi.org/10.1186/s12915-017-0457-4 JAN 11 2018
  • Nature's genetic screens: using genome-wide association studies for effector discovery 
    Sanchez-Vallet, Andrea; Hartmann, Fanny E.; Marcel, Thierry C.; et al. 
    MOLECULAR PLANT PATHOLOGY, 19 (1): 3-6 https://doi.org/10.1111/mpp.12592 JAN 2018
  • Quantitative trait locus mapping reveals complex genetic architecture of quantitative virulence in the wheat pathogen Zymoseptoria tritici 
    Stewart, Ethan L.; Croll, Daniel; Lendenmann, Mark H.; et al. 
    MOLECULAR PLANT PATHOLOGY, 19 (1): 201-216 https://doi.org/10.1111/mpp.12515 JAN 2018

Prof. Dr. Daniel Croll
University of Neuch√Ętel
Institute of Biology
2000 Neuch√Ętel

Tel. +41 (0)32 718 23 37

Research topics

  • Genetic basis of pathogen virulence
  • Ecological genomics and local adaptation of pathogens
  • Population genomics of pathogen outbreaks
  • Structure and evolution of pathogen genomes
  • Transposable elements and the evolution of gene regulation


  • Crop resistance breeding
  • Bioinformatics and genome assembly
  • Molecular plant pathology
  • Fungal community analyses
  • Genome-wide association mapping (GWAS)