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.
- 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
- 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)