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

Abstract

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.

Authors:
ORCiD logo [1];  [2];  [1];  [1];  [1];  [1];  [1];  [1];  [1];  [1];  [1];  [1];  [3];  [4];  [5];  [6]; ORCiD logo [2];  [1]
  1. Univ. of Ottawa, Ottawa, ON (Canada)
  2. Inst. National de la Recherche Agronomique (INRA), Champenoux (France)
  3. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  4. Aix-Marseille Univ., Marseille (France); Inst. National de la Recherche Agronomique (INRA), Marseille (France)
  5. Aix-Marseille Univ., Marseille (France); Inst. National de la Recherche Agronomique (INRA), Marseille (France); King Abdulaziz Univ., Jeddah (Saudi Arabia)
  6. Univ. de Toulouse, Castanet-Tolosan (France)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC); Univ. of California, Oakland, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1543996
Alternate Identifier(s):
OSTI ID: 1481337
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
New Phytologist
Additional Journal Information:
Journal Volume: 220; Journal Issue: 4; Journal ID: ISSN 0028-646X
Publisher:
Wiley
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Plant Sciences; arbuscular mycorrhizal fungi (AMF); gene exchange; intraspecific variation; pan-genome; Rhizophagus irregularis; transposable elements

Citation Formats

Chen, Eric C. H., Morin, Emmanuelle, Beaudet, Denis, Noel, Jessica, Yildirir, Gokalp, Ndikumana, Steve, Charron, Philippe, St-Onge, Camille, Giorgi, John, Krüger, Manuela, Marton, Timea, Ropars, Jeanne, Grigoriev, Igor V., Hainaut, Matthieu, Henrissat, Bernard, Roux, Christophe, Martin, Francis, and Corradi, Nicolas. High intraspecific genome diversity in the model arbuscular mycorrhizal symbiont Rhizophagus irregularis. United States: N. p., 2018. Web. doi:10.1111/nph.14989.
Chen, Eric C. H., Morin, Emmanuelle, Beaudet, Denis, Noel, Jessica, Yildirir, Gokalp, Ndikumana, Steve, Charron, Philippe, St-Onge, Camille, Giorgi, John, Krüger, Manuela, Marton, Timea, Ropars, Jeanne, Grigoriev, Igor V., Hainaut, Matthieu, Henrissat, Bernard, Roux, Christophe, Martin, Francis, & Corradi, Nicolas. High intraspecific genome diversity in the model arbuscular mycorrhizal symbiont Rhizophagus irregularis. United States. doi:10.1111/nph.14989.
Chen, Eric C. H., Morin, Emmanuelle, Beaudet, Denis, Noel, Jessica, Yildirir, Gokalp, Ndikumana, Steve, Charron, Philippe, St-Onge, Camille, Giorgi, John, Krüger, Manuela, Marton, Timea, Ropars, Jeanne, Grigoriev, Igor V., Hainaut, Matthieu, Henrissat, Bernard, Roux, Christophe, Martin, Francis, and Corradi, Nicolas. Mon . "High intraspecific genome diversity in the model arbuscular mycorrhizal symbiont Rhizophagus irregularis". United States. doi:10.1111/nph.14989. https://www.osti.gov/servlets/purl/1543996.
@article{osti_1543996,
title = {High intraspecific genome diversity in the model arbuscular mycorrhizal symbiont Rhizophagus irregularis},
author = {Chen, Eric C. H. and Morin, Emmanuelle and Beaudet, Denis and Noel, Jessica and Yildirir, Gokalp and Ndikumana, Steve and Charron, Philippe and St-Onge, Camille and Giorgi, John and Krüger, Manuela and Marton, Timea and Ropars, Jeanne and Grigoriev, Igor V. and Hainaut, Matthieu and Henrissat, Bernard and Roux, Christophe and Martin, Francis and Corradi, Nicolas},
abstractNote = {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.},
doi = {10.1111/nph.14989},
journal = {New Phytologist},
number = 4,
volume = 220,
place = {United States},
year = {2018},
month = {1}
}

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