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.

• Screening of grapevine red blotch virus in two European ampelographic collections
  Reynard, Jean-Sebastien; Brodard, Justine; Dubuis, Nathalie; Kellenberger, Isabelle; Spilmont, Anne-Sophie; et al.
  Journal Of Plant Pathology 10.1007/s42161-021-00952-9  NOV 2021
• Population-level deep sequencing reveals the interplay of clonal and sexual reproduction in the fungal wheat pathogen Zymoseptoria tritici
  Singh, Nikhil Kumar; Karisto, Petteri; Croll, Daniel
  Microbial Genomics 10.1099/mgen.0.000678  OCT 2021
• A robust sequencing assay of a thousand amplicons for the high-throughput population monitoring of Alpine ibex immunogenetics
  Kessler, Camille; Brambilla, Alice; Waldvogel, Dominique; Camenisch, Glauco; Biebach, Iris; et al.
  Molecular Ecology Resources10.1111/1755-0998.13452  JAN 2022
• Transcriptome-wide SNPs for Botrychium lunaria ferns enable fine-grained analysis of ploidy and population structure
  Mossion, Vinciane; Dauphin, Benjamin; Grant, Jason; Kessler, Michael; Zemp, Niklaus; Croll, Daniel
  Molecular Ecology Resources 10.1111/1755-0998.13478  JAN 2022
• A new method to determine the diet of pygmy hippopotamus in Tai National Park, Cote d'Ivoire
  Hendier, Alba; Chatelain, Cyrille; Du Pasquier, Pierre-Emmanuel; Paris, Monique; Ouattara, Karim; et al.
  African Journal Of Ecology 10.1111/aje.12888 DEC 2021
• Soil composition and plant genotype determine benzoxazinoid-mediated plant-soil feedbacks in cereals
  Cadot, Selma; Gfeller, Valentin; Hu, Lingfei; Singh, Nikhil; Sanchez-Vallet, Andrea; Glauser, Gaetan; Croll, Daniel; Erb, Matthias; van der Heijden, Marcel G. A.; Schlaeppi, Klaus
  Plant Cell And Environment  10.1111/pce.14184  DEC 2021
• Cryptic genetic structure and copy-number variation in the ubiquitous forest symbiotic fungus Cenococcum geophilum
  Dauphin, Benjamin; Pereira, Maira de Freitas; Kohler, Annegret; Grigoriev, Igor, V; Barry, Kerrie; et al.
  Environmental Microbiology 10.1111/1462-2920.15752  NOV 2021
• A population-level invasion by transposable elements triggers genome expansion in a fungal pathogen
  Oggenfuss, Ursula; Badet, Thomas; Wicker, Thomas; Hartmann, Fanny E.; Singh, Nikhil Kumar; Abraham, Leen; Karisto, Petteri; Vonlanthen, Tiziana; Mundt, Christopher; McDonald, Bruce A.; Croll, Daniel
  Elife 10.7554/eLife.69249 SEP 16 2021
• Genome-wide association study for septoria tritici blotch resistance reveals the occurrence and distribution of Stb6 in a historic Swiss landrace collection (vol 217, 108, 2021)
  Dutta, Anik; Croll, Daniel; McDonald, Bruce A.; Krattinger, Simon G.
  Euphytica 10.1007/s10681-021-02906-9 SEP 2021
• Population genomics of transposable element activation in the highly repressive genome of an agricultural pathogen
  Pereira, Danilo; Oggenfuss, Ursula; McDonald, Bruce A.; Croll, Daniel
  Microbial Genomics 10.1099/mgen.0.000540  AUG 2021
• Genome-scale phylogenies reveal relationships among Parastagonospora species infecting domesticated and wild grasses
  Croll, D.; Crous, P. W.; Pereira, D.; Mordecai, E. A.; McDonald, B. A.; Brunner, P. C.
  Persoonia 10.3767/persoonia.2021.46.04 JUN 2021
• Machine-learning predicts genomic determinants of meiosis-driven structural variation in a eukaryotic pathogen
  Badet, Thomas; Fouche, Simone; Hartmann, Fanny E.; Zala, Marcello; Croll, Daniel
  Nature Communications 10.1038/s41467-021-23862-x JUN 10 2021
• Rapid sequence evolution driven by transposable elements at a virulence locus in a fungal wheat pathogen
  Singh, Nikhil Kumar; Badet, Thomas; Abraham, Leen; Croll, Daniel
  Bmc Genomics10.1186/s12864-021-07691-2  MAY 27 2021
• Mapping the adaptive landscape of a major agricultural pathogen reveals evolutionary constraints across heterogeneous environments
  Dutta, Anik; Hartmann, Fanny E.; Francisco, Carolina Sardinha; McDonald, Bruce A.; Croll, Daniel
  Isme Journal, 10.1038/s41396-020-00859-w  MAY 2021
• Emergence and diversification of a highly invasive chestnut pathogen lineage across southeastern Europe
  Stauber, Lea; Badet, Thomas; Feurtey, Alice; Prospero, Simone; Croll, Daniel
  Elife,   10.7554/eLife.56279  MAR 5 2021
• …

• The Genetic Architecture of Emerging Fungicide Resistance in Populations of a Global Wheat Pathogen
  Pereira, Danilo; McDonald, Bruce A.; Croll, Daniel
  Genome Biology And Evolution,  10.1093/gbe/evaa203   DEC 2020
• The complex genomic basis of rapid convergent adaptation to pesticides across continents in a fungal plant pathogen
  Hartmann, Fanny E.; Vonlanthen, Tiziana; Singh, Nikhil Kumar; McDonald, Megan C.; Milgate, Andrew; et al.
  Molecular Ecology, 10.1111/mec.15737   DEC 2020
• Tackling microbial threats in agriculture with integrative imaging and computational approaches
  Singh, Nikhil Kumar; Dutta, Anik; Puccetti, Guido; Croll, Daniel
  Computational And Structural Biotechnology Journal 10.1016/j.csbj.2020.12.018  2020
• A Chromosome-Scale Genome Assembly for the Fusarium oxysporum Strain Fo5176 To Establish a Model Arabidopsis-Fungal Pathosystem
  Fokkens, Like; Guo, Li; Dora, Susanne; Wang, Bo; Ye, Kai; Sanchez-Rodriguez, Clara; Croll, Daniel
  G3-genes Genomes Genetics   DOI: 10.1534/g3.120.401375  OCT 2020
• Transcriptome plasticity underlying plant root colonization and insect invasion by Pseudomonas protegens
  Vesga, Pilar; Flury, Pascale; Vacheron, Jordan; Keel, Christoph; Croll, Daniel; Maurhofer M
  Isme Journal  DOI: 10.1038/s41396-020-0729-9    NOV 2020
• A Chromosome-Scale Genome Assembly for the Fusarium oxysporum Strain Fo5176 To Establish a Model Arabidopsis-Fungal Pathosystem
  Fokkens, Like; Guo, Li; Dora, Susanne; Wang, Bo; Ye, Kai; Sanchez-Rodriguez, Clara; Croll, Daniel
  G3-genes Genomes Genetics 10.1534/g3.120.401375 OCT 2020
• Comparative Genomics Analyses of Lifestyle Transitions at the Origin of an Invasive Fungal Pathogen in the Genus Cryphonectria
  Stauber, Lea; Prospero, Simone; Croll, Daniel
  Msphere  DOI: 10.1128/mSphere.00737-20  SEP-OCT 2020
• Maintenance of variation in virulence and reproduction in populations of an agricultural plant pathogen
  Dutta, Anik; Croll, Daniel; McDonald, Bruce A.; Barrett, Luke G.
  Evolutionary Applications  DOI: 10.1111/eva.13117 SEP 2020
• The rise and fall of genes: origins and functions of plant pathogen pangenomes
  Badet, Thomas; Croll, Daniel
  Current Opinion In Plant Biology  DOI: 10.1016/j.pbi.2020.04.009  AUG 2020
• Genome compartmentalization predates species divergence in the plant pathogen genus Zymoseptoria
  Feurtey, Alice; Lorrain, Cecile; Croll, Daniel; Eschenbrenner, Christoph; Freitag, Michael; et al.
  Bmc Genomics  DOI: 10.1186/s12864-020-06871-w  AUG 26 2020
• Natural selection drives population divergence for local adaptation in a wheat pathogen
  Pereira, Danilo; Croll, Daniel; Brunner, Patrick C.; McDonald, Bruce A.
  Fungal Genetics And Biology  DOI: 10.1016/j.fgb.2020.103398  AUG 2020
• A secreted LysM effector protects fungal hyphae through chitin-dependent homodimer polymerization
  Sanchez-Vallet, Andrea; Tian, Hui; Rodriguez-Moreno, Luis; Valkenburg, Dirk-Jan; Saleem-Batcha, Raspudin; et al.
  Plos Pathogens  DOI: 10.1371/journal.ppat.1008652  JUN 2020
• 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
• 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
• 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
• …

• 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)