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New Phytol. 2018 Dec;220(4):1161-1171. doi: 10.1111/nph.14989. Epub 2018 Jan 22.

High intraspecific genome diversity in the model arbuscular mycorrhizal symbiont Rhizophagus irregularis.

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Department of Biology, University of Ottawa, Ottawa, ON, K1N9A7, Canada.
Institut National de la Recherche Agronomique (INRA), Unité Mixte de Recherche 1136 Interactions Arbres/Microorganismes, Laboratoire D'excellence Recherches Avancées sur la Biologie de l'Arbre et les Ecosystèmes Forestiers (ARBRE), Centre INRA-Grand Est-Nancy, Champenoux, 54280, France.
US Department of Energy Joint Genome Institute (JGI), Walnut Creek, CA, 94598, USA.
Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, Marseille, 13288, France.
INRA, USC 1408 AFMB, Marseille, F-13288, France.
Department of Biological Sciences, King Abdulaziz University, Jeddah, 21589, Saudi Arabia.
Laboratoire de Recherche en Sciences Végétales, UPS, CNRS 24 Chemin de Borde Rouge-Auzeville, Université de Toulouse, Castanet-Tolosan, 31326, France.


Arbuscular mycorrhizal fungi (AMF) are known to improve plant fitness through the establishment of mycorrhizal symbioses. Genetic and phenotypic variations among closely related AMF isolates can significantly affect plant growth, but the genomic changes underlying this variability are unclear. To address this issue, we improved the genome assembly and gene annotation of the model strain Rhizophagus irregularis DAOM197198, and compared its gene content with five isolates of R. irregularis sampled in the same field. All isolates harbor striking genome variations, with large numbers of isolate-specific genes, gene family expansions, and evidence of interisolate genetic exchange. The observed variability affects all gene ontology terms and PFAM protein domains, as well as putative mycorrhiza-induced small secreted effector-like proteins and other symbiosis differentially expressed genes. High variability is also found in active transposable elements. Overall, these findings indicate a substantial divergence in the functioning capacity of isolates harvested from the same field, and thus their genetic potential for adaptation to biotic and abiotic changes. Our data also provide a first glimpse into the genome diversity that resides within natural populations of these symbionts, and open avenues for future analyses of plant-AMF interactions that link AMF genome variation with plant phenotype and fitness.


Rhizophagus irregularis ; arbuscular mycorrhizal fungi (AMF); gene exchange; intraspecific variation; pan-genome; transposable elements


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