title: Using Population and Comparative Genomics to Understand the Genetic Basis of Effector-Driven Fungal Pathogen Evolution.
abstract: Epidemics caused by fungal plant pathogens pose a major threat to agro-ecosystems and impact global food security. High-throughput sequencing enabled major advances in understanding how pathogens cause disease on crops. Hundreds of fungal genomes are now available and analyzing these genomes highlighted the key role of effector genes in disease. Effectors are small secreted proteins that enhance infection by manipulating host metabolism. Fungal genomes carry 100s of putative effector genes, but the lack of homology among effector genes, even for closely related species, challenges evolutionary and functional analyses. Furthermore, effector genes are often found in rapidly evolving chromosome compartments which are difficult to assemble. We review how population and comparative genomics toolsets can be combined to address these challenges. We highlight studies that associated genome-scale polymorphisms with pathogen lifestyles and adaptation to different environments. We show how genome-wide association studies can be used to identify effectors and other pathogenicity-related genes underlying rapid adaptation. We also discuss how the compartmentalization of fungal genomes into core and accessory regions shapes the evolution of effector genes. We argue that an understanding of genome evolution provides important insight into the trajectory of host-pathogen co-evolution.
authors.affiliation: Plant Pathology, Institute of Integrative Biology, ETH ZurichZurich, Switzerland; UMR, BIOGER, INRA, AgroParisTech, Université Paris-SaclayThiverval-Grignon, France.
authors.forename: Clémence
authors.initials: C
authors.lastname: Plissonneau
authors.affiliation: College of Agriculture "Luiz de Queiroz", University of São Paulo São Paulo, Brazil.
authors.forename: Juliana
authors.initials: J
authors.lastname: Benevenuto
authors.affiliation: Plant Pathology, Institute of Integrative Biology, ETH ZurichZurich, Switzerland; School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan MalaysiaSelangor, Malaysia.
authors.forename: Norfarhan
authors.initials: N
authors.lastname: Mohd-Assaad
authors.affiliation: Plant Pathology, Institute of Integrative Biology, ETH Zurich Zurich, Switzerland.
authors.forename: Simone
authors.initials: S
authors.lastname: Fouché
authors.affiliation: Plant Pathology, Institute of Integrative Biology, ETH Zurich Zurich, Switzerland.
authors.forename: Fanny E
authors.initials: FE
authors.lastname: Hartmann
authors.affiliation: Plant Pathology, Institute of Integrative Biology, ETH ZurichZurich, Switzerland; Laboratory of Evolutionary Genetics, Institute of Biology, University of NeuchatelNeuchatel, Switzerland.
authors.forename: Daniel
authors.initials: D
authors.lastname: Croll
keywords: agricultural ecosystems; association mapping studies; evolution; fungi; genome; molecular; plant pathogens; population genomics