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Evidence for the sexual origin of heterokaryosis in arbuscular mycorrhizal fungi

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.

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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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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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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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