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.
Highlights
Fungal plant pathogens are major threats to modern agricultural ecosystems and global food security (Strange and Scott, 2005)
The recent broad accessibility of genome sequencing technologies enabled genome-scale analyses of a rapidly growing number of plant pathogen species. These analyses revealed major factors contributing to disease emergence and made plant pathogenic fungi some of the best-studied models of pathogen evolution
Research over the past decades showed that gene-forgene model (GFG) interactions govern many host–plant pathogen interactions, identifying the effector genes involved in the interaction is still challenging
Summary
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 available and analyzing these genomes highlighted the key role of effector genes in disease. 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. 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 discuss how the compartmentalization of fungal genomes into core and accessory regions shapes the evolution of effector genes.
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