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

  • Chromosomal assembly and analyses of genome-wide recombination rates in the forest pathogenic fungus Armillaria ostoyae
    Heinzelmann, Renate; Rigling, Daniel; Sipos, Gyorgy; Muensterkoetter, Martin; Croll, Daniel
    Heredity  DOI: 10.1038/s41437-020-0306-z   MAR 2020
  • Purging of highly deleterious mutations through severe bottlenecks in Alpine ibex
    Grossen, Christine; Guillaume, Frederic; Keller, Lukas F.; Croll, Daniel
    Nature Communications,  11(1) Number: 1001  DOI: 10.1038/s41467-020-14803-1  FEB 21 2020
  • Stress-Driven Transposable Element De-repression Dynamics and Virulence Evolution in a Fungal Pathogen
    Fouche, Simone; Badet, Thomas; Oggenfuss, Ursula; Plissonneau, Clemence; Francisco, Carolina Sardinha; Croll Daniel
    Molecular Biology And Evolution  DOI: 10.1093/molbev/msz216  JAN 2020
  • A 19-isolate reference-quality global pangenome for the fungal wheat pathogen Zymoseptoria tritici
    Badet, Thomas; Oggenfuss, Ursula; Abraham, Leen; McDonald, Bruce A.; Croll, Daniel
    Bmc Biology 18(1) Article Number: 12 DOI: 10.1186/s12915-020-0744-3  FEB 11 2020
  • Complex Evolutionary Origins of Specialized Metabolite Gene Cluster Diversity among the Plant Pathogenic Fungi of the Fusarium graminearum Species Complex
    Tralamazza, Sabina Moser; Rocha, Liliana Oliveira; Oggenfuss, Ursula; Correa, Benedito; Croll, Daniel
    Genome Biology And Evolution, 10.1093/gbe/evz225, NOV 2019
  • The emergence of the multi-species NIP1 effector in Rhynchosporium was accompanied by high rates of gene duplications and losses
    Mohd-Assaad, N; McDonald, BA; Croll, D
    ENVIRONMENTAL MICROBIOLOGY, 21 (8):2677-2695; 10.1111/1462-2920.14583 AUG 2019
  • 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

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)