Using population and comparative genomics to understand the genetic basis of effector-driven fungal pathogen evolution

Clémence Plissonneau, Juliana Benevenuto, Norfarhan Mohd Assa`Ad, Simone Fouché, Fanny E. Hartmann, Daniel Croll

Research output: Contribution to journalReview article

26 Citations (Scopus)

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.

Original languageEnglish
Article number119
JournalFrontiers in Plant Science
Volume8
Issue numberFEBRUARY
DOIs
Publication statusPublished - 3 Feb 2017

Fingerprint

genomics
genome
pathogens
genes
food defense
coevolution
plant pathogens
lifestyle
trajectories
pathogenicity
genetic polymorphism
chromosomes
metabolism
ecosystems
crops
infection
proteins

Keywords

  • Agricultural ecosystems
  • Association mapping studies
  • Evolution
  • Fungi
  • Genome
  • Molecular
  • Plant pathogens
  • Population genomics

ASJC Scopus subject areas

  • Plant Science

Cite this

Using population and comparative genomics to understand the genetic basis of effector-driven fungal pathogen evolution. / Plissonneau, Clémence; Benevenuto, Juliana; Mohd Assa`Ad, Norfarhan; Fouché, Simone; Hartmann, Fanny E.; Croll, Daniel.

In: Frontiers in Plant Science, Vol. 8, No. FEBRUARY, 119, 03.02.2017.

Research output: Contribution to journalReview article

Plissonneau, Clémence ; Benevenuto, Juliana ; Mohd Assa`Ad, Norfarhan ; Fouché, Simone ; Hartmann, Fanny E. ; Croll, Daniel. / Using population and comparative genomics to understand the genetic basis of effector-driven fungal pathogen evolution. In: Frontiers in Plant Science. 2017 ; Vol. 8, No. FEBRUARY.
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