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Nat Commun. 2016 May 6;7:11362. doi: 10.1038/ncomms11362.

Survival trade-offs in plant roots during colonization by closely related beneficial and pathogenic fungi.

Author information

  • 1Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany.
  • 2German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany.
  • 3Computational Biology of Infection Research, Helmholtz Center for Infection Research, 38124 Braunschweig, Germany.
  • 4Max-von-Pettenkofer Institute, LMU Munich, German Center for Infection Research (DZIF), Partner Site LMU Munich, 80336 Munich, Germany.
  • 5Department of Algorithmic Bioinformatics, Heinrich Heine University Duesseldorf, 40225 Duesseldorf, Germany.
  • 6Cluster of Excellence on Plant Sciences (CEPLAS), Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany.
  • 7Instituto Hispano-Luso de Investigaciones Agrarias (CIALE), Departamento de Microbiología y Genética, Universidad de Salamanca, 37185 Villamayor, Spain.
  • 8CBS-KNAW Fungal Biodiversity Centre, 3584 CT Utrecht, The Netherlands.
  • 9UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, 78850 Thiverval-Grignon, France.
  • 10CNRS UMR 7257, Aix-Marseille University, 13288 Marseille, France.
  • 11INRA, USC 1408 AFMB, 13288 Marseille, France.
  • 12Department of Biological Sciences, King Abdulaziz University, 21589 Jeddah, Saudi Arabia.
  • 13Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, 91405 Orsay, France.
  • 14Laboratoire de Recherche en Informatique, CNRS, Université Paris-Sud, 91405 Orsay, France.
  • 15Centro de Biotecnología y Genómica de Plantas (UPM-INIA) and E.T.S.I. Agrónomos, Universidad Politécnica de Madrid Campus de Montegancedo, 28223 Madrid, Spain.


The sessile nature of plants forced them to evolve mechanisms to prioritize their responses to simultaneous stresses, including colonization by microbes or nutrient starvation. Here, we compare the genomes of a beneficial root endophyte, Colletotrichum tofieldiae and its pathogenic relative C. incanum, and examine the transcriptomes of both fungi and their plant host Arabidopsis during phosphate starvation. Although the two species diverged only 8.8 million years ago and have similar gene arsenals, we identify genomic signatures indicative of an evolutionary transition from pathogenic to beneficial lifestyles, including a narrowed repertoire of secreted effector proteins, expanded families of chitin-binding and secondary metabolism-related proteins, and limited activation of pathogenicity-related genes in planta. We show that beneficial responses are prioritized in C. tofieldiae-colonized roots under phosphate-deficient conditions, whereas defense responses are activated under phosphate-sufficient conditions. These immune responses are retained in phosphate-starved roots colonized by pathogenic C. incanum, illustrating the ability of plants to maximize survival in response to conflicting stresses.

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