Using Population and Comparative Genomics to Understand the Genetic Basis of Effector-Driven Fungal Pathogen Evolution
2017
Plissonneau, Clémence | Benevenuto, Juliana | Mohd-Assaad, Norfarhan | Fouche, Simone | Hartmann, Fanny E. | Croll, Daniel | BIOlogie et GEstion des Risques en agriculture (BIOGER) ; Institut National de la Recherche Agronomique (INRA)-AgroParisTech | Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich) | Coll Agr Luiz de Queiroz ; Universidade de São Paulo = University of São Paulo (USP) | Universiti Kebangsaan Malaysia (UKM) | Institute of Biology of the University of Neuchâtel ; Université de Neuchâtel = University of Neuchatel (UNINE) | Contrat Jeune Scientifique) from INRA. N.M was supported by the Ministry of Higher Education Malaysia (MOHE) and Universiti Kebangsaan Malaysia (UKM) under the SLAI scheme. FH was funded by the ETH Zurich Research Grant,São Paulo Research Foundation (FAPESP, grant number: 2016/03768-5).
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.
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