Evolutionary genomics of plant-pathogen interactions

Evolutionary Genetics

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 Publications

  • Cautionary Notes on Use of the MoT3 Diagnostic Assay for Magnaporthe oryzae Wheat and Rice Blast Isolates
    Gupta, DR; Avila, CSR; Win, J; Soanes, DM; Ryder, LS; Croll, D; Bhattacharjee, P; Hossain, MS; Mahmud, NU; Mehebub, MS; Surovy, MZ; Rahman, MM; Talbot, NJ; Kamoun, S; Islam, MT
    PHYTOPATHOLOGY, 109 (4):504-508; 10.1094/PHYTO-06-18-0199-LE APR 2019
  • Wheat blast: from its origins in South America to its emergence as a global threat
    Ceresini, PC; Castroagudin, VL; Rodrigues, FA; Rios, JA; Aucique-Perez, CE; Moreira, SI; Croll, D; Alves, E; de Carvalho, G; Maciel, JLN; McDonald, BA
    MOLECULAR PLANT PATHOLOGY, 20 (2):155-172; 10.1111/mpp.12747 FEB 2019
  • Rapid Parallel Evolution of Azole Fungicide Resistance in Australian Populations of the Wheat Pathogen Zymoseptoria tritici
    McDonald, MC; Renkin, M; Spackman, M; Orchard, B; Croll, D; Solomon, CPS; Milgate, A
  • The birth and death of effectors in rapidly evolving filamentous pathogen genomes
    Fouche, S; Plissonneau, C; Croll, D
    CURRENT OPINION IN MICROBIOLOGY, 46 34-42; 10.1016/j.mib.2018.01.020 DEC 2018
  • The Monothiol Glutaredoxin Grx4 Regulates Iron Homeostasis and Virulence in Cryptococcus neoformans
    Attarian, R; Hu, GG; Sanchez-Leon, E; Caza, M; Croll, D; Do, E; Bach, H; Missall, T; Lodge, J; Jung, WH; Kronstad, JW
    MBIO, 9 (6):10.1128/mBio.02377-18 NOV-DEC 2018
  • Wheat Blast: Past, Present, and Future
    Ceresini, PC; Castroagudin, VL; Rodrigues, FA; Rios, JA; Aucique-Perez, CE; Moreira, SI; Alves, E; Croll, D; Maciel, JLN
    Edited by: Leach JE; Lindow SE
    ANNUAL REVIEW OF PHYTOPATHOLOGY, VOL 56, 56 427-456; 10.1146/annurev-phyto-080417-050036 2018
  • The Genome Biology of Effector Gene Evolution in Filamentous Plant Pathogens
    Sanchez-Vallet, A; Fouche, S; Fudal, I; Hartmann, FE; Soyer, JL; Tellier, A; Croll, D Edited by: Leach JE; Lindow SE
    ANNUAL REVIEW OF PHYTOPATHOLOGY, VOL 56, 56 21-40; 10.1146/annurev-phyto-080516-035303 2018
  • Genomewide signatures of selection in Epichloe reveal candidate genes for host specialization
    Schirrmann, Melanie K; Zoller, Stefan; Croll, Daniel; Stukenbrock, EH; Leuchtmann, A; Fior, S
    MOLECULAR ECOLOGY   Volume: 27   Issue: 15   Pages: 3070-3086 10.1111/mec.14585 AUG 2018
  • Genome-Wide Detection of Genes Under Positive Selection in Worldwide Populations of the Barley Scald Pathogen
    Mohd-Assaad, N; McDonald, BA; Croll, D
    GENOME BIOLOGY AND EVOLUTION, 10 (5):1315-1332; 10.1093/gbe/evy087 MAY 2018
  • Meiosis Leads to Pervasive Copy-Number Variation and Distorted Inheritance of Accessory Chromosomes of the Wheat Pathogen Zymoseptoria tritici
    Fouche, S; Plissonneau, C; McDonald, BA; Croll, D
    GENOME BIOLOGY AND EVOLUTION, 10 (6):1416-1429; 10.1093/gbe/evy100 JUN 2018
  • A fungal avirulence factor encoded in a highly plastic genomic region triggers partial resistance to septoria tritici blotch
    Meile L; Croll D; Brunner PC; Plissonneau C; Hartmann FE; McDonald BA; Sanchez-Vallet A
    NEW PHYTOLOGIST   Volume: 219   Issue: 3 1048-1061 10.1111/nph.15180   AUG 2018
  • Transposable element insertions shape gene regulation and melanin production in a fungal pathogen of wheat
    Krishnan, Parvathy; Meile, Lukas; Plissonneau, Clemence; Ma, Xin; Hartmann, Fanny E; Croll, Daniel; McDonald, Bruce A; Sanchez-Vallet, Andrea
    BMC BIOLOGY   Volume: 16(78)  10.1186/s12915-018-0543-2  JUL 16 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, 27 (12):2725-2741; 10.1111/mec.14711 JUN 2018
  • A monothiol glutaredoxin is required for iron homeostasis and virulence in the AIDS-associated pathogen Cryptococcus neoformans
    Hu, GG; Attarian, R; Do, E; Croll, D; Caza, M; Bach, H; Missall, TA; Lodge, J; Jung, WH; Kronstad, JW
    MEDICAL MYCOLOGY, 56 S124-S124; 2 JUN 2018
  • 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
  • Population genomics analyses of European ibex species show lower diversity and higher inbreeding in reintroduced populations 
    Grossen, Christine; Biebach, Iris; Angelone-Alasaad, Samer; Keller, LF ; Croll, D
    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 30

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)