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Evidence for the sexual origin of heterokaryosis in arbuscular mycorrhizal fungi

Nature Microbiology volume 1, Article number: 16033 (2016) Cite this article

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Abstract

Sexual reproduction is ubiquitous among eukaryotes, and fully asexual lineages are extremely rare. Prominent among ancient asexual lineages are the arbuscular mycorrhizal fungi (AMF), a group of plant symbionts with a multinucleate cytoplasm. Genomic divergence among co-existing nuclei was proposed to drive the evolutionary success of AMF in the absence of sex1, but this hypothesis has been contradicted by recent genome analyses that failed to find significant genetic diversity within an AMF isolate2,3. Here, we set out to resolve issues surrounding the genome organization and sexual potential of AMF by exploring the genomes of five isolates of Rhizophagus irregularis, a model AMF. We find that genetic diversity in this species varies among isolates and is structured in a homo-dikaryon-like manner usually linked with the existence of a sexual life cycle. We also identify a putative AMF mating-type locus, containing two genes with structural and evolutionary similarities with the mating-type locus of some Dikarya. Our analyses suggest that this locus may be multi-allelic and that AMF could be heterothallic and bipolar. These findings reconcile opposing views on the genome organization of these ubiquitous plant symbionts and open avenues for strain improvement and environmental application of these organisms.

The maintenance of sexual reproduction remains a fundamental question in evolutionary biology, as it induces fitness costs through energetic genetic transmission and demographic constraints4, but is also essential for the long-term persistence and adaptation of eukaryotic species5. Eukaryotes relying exclusively on asexual reproduction are considered to be exceptional and, at present, only a few ‘ancient asexual’ lineages are described in the literature6, including the arbuscular mycorrhizal fungi (AMF). These microorganisms establish symbiotic associations with terrestrial plant roots, thereby improving their nutrient uptake, growth and tolerance to environmental stresses7, and are thought to have played a crucial role in the colonization of land by plants8.

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Figure 1: Allele frequency plots and flow cytometry analyses for isolates A1, A4, A5, B3 and C2.
Figure 2: Genomic architecture of putative AMF mating-type locus in R. irregularis.
Figure 3: Single nuclear analysis of MAT alleles and SNPs in A1, C2 and A5 isolates.
Figure 4: Phylogeny of MAT-locus alleles in Rhizophagus spp and a model of the putative cycle of Rhizophagus spp.

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Acknowledgements

The authors thank J.W. Taylor, T. James, D. Beaudet, T. Giraud, M. Lόpez-Villavicencio and I. de la Providencia, for constructive comments and suggestions on previous versions of this manuscript. The authors also thank I. Sanders (University of Lausanne) and Y. Dalpé (Agriculture Canada, Ottawa) for providing the in vitro isolates of Rhizophagus irregularis used in this study, M. Griesmann (Faculty of Biology, LMU Munich) for help with the BUSCO analyses and S. Dreissig (IPK, Gatersleben) for help with WGA work. N.C. is a fellow of the Canadian Institute for Advanced Research. N.C.'s work is supported by the Discovery programme from the Natural Sciences and Engineering Research Council of Canada (NSERC-Discovery), an Early Researcher Award from the Ontario Ministry of Research and Innovation (ER13-09-190) and the ZygoLife project funded by the National Science Foundation (DEB 1441677). M.K. was financed by the European Social Fund (ESF) and the state budget of Czech Republic through the Operational Programme Education for Competitiveness (OPEC) under project number CZ.1.07/2.3.00/30.0048.

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Author notes

  1. Jeanne Ropars and Kinga Sędzielewska Toro: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Biology, Canadian Institute for Advanced Research, University of Ottawa, Ottawa, Ontario, Canada

    Jeanne Ropars, Jessica Noel, Adrian Pelin, Philippe Charron, Timea Marton, Manuela Krüger & Nicolas Corradi

  2. LMU Munich, Faculty of Biology, Genetics, D-82152 Planegg-Martinsried, Germany

    Kinga Sędzielewska Toro & Andreas Brachmann

  3. FASTERIS S.A., Ch. du Pont-du-Centenaire 109, PO Box 28, CH-1228 Plan-les-Ouates, Switzerland

    Laurent Farinelli

  4. Institute of Botany, Academy of Sciences of the Czech Republic, Zámek 1, Průhonice, CZ-25243, Czech Republic

    Manuela Krüger

  5. Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany

    Jörg Fuchs

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  1. Jeanne Ropars
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Contributions

J.R., K.S.T., A.B. and N.C. planned the experiments. J.R., K.S.T., J.N., P.C., L.F., T.M., M.K. and J.F. performed experiments. J.R., A.P., A.B. and N.C. performed bioinformatic analyses. J.R. and N.C. drafted the manuscript with contributions from K.S.T. and A.B.

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Correspondence to Nicolas Corradi.

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Supplementary Figures 1-10, Tables 1-4 and 7 (PDF 21415 kb)

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Supplementary Table 6 (XLSX 44 kb)

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Ropars, J., Toro, K., Noel, J. et al. Evidence for the sexual origin of heterokaryosis in arbuscular mycorrhizal fungi. Nat Microbiol 1, 16033 (2016). https://doi.org/10.1038/nmicrobiol.2016.33

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