Cryptic genetic structure and copy-number variation in the ubiquitous forest symbiotic fungus Cenococcum geophilum

Dauphin, Benjamin; Freitas Pereira, Maíra; Kohler, Annegret; Grigoriev, Igor V.; Barry, Kerrie; Na, Hyunsoo; Amirebrahimi, Mojgan; Lipzen, Anna; Martin, Francis; Peter, Martina; Croll, Daniel

doi:10.1111/1462-2920.15752

Title: Cryptic genetic structure and copy-number variation in the ubiquitous forest symbiotic fungus Cenococcum geophilum

Journal Article · 31 August 2021 · Environmental Microbiology

DOI: https://doi.org/10.1111/1462-2920.15752 · OSTI ID:1904114

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^[5]; Na, Hyunsoo ^[5]; Amirebrahimi, Mojgan ^[5]; Lipzen, Anna ^[5];

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Swiss Federal Research Institute, Birmensdorf (Switzerland); OSTI
Swiss Federal Research Institute, Birmensdorf (Switzerland); Universite de Lorraine, Champenoux (France)
Universite de Lorraine, Champenoux (France)
University of California, Berkeley, CA (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). Joint Genome Institute
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). Joint Genome Institute
Swiss Federal Research Institute, Birmensdorf (Switzerland)
University of Neuchâtel (Switzerland)

Ectomycorrhizal (ECM) fungi associated with plants constitute one of the most successful symbiotic interactions in forest ecosystems. ECM support trophic exchanges with host plants and are important factors for the survival and stress resilience of trees. However, ECM clades often harbour morpho-species and cryptic lineages, with weak morphological differentiation. How this relates to intraspecific genome variability and ecological functioning is poorly known. Here, we analysed 16 European isolates of the ascomycete Cenococcum geophilum, an extremely ubiquitous forest symbiotic fungus with no known sexual or asexual spore-forming structures but with a massively enlarged genome. We carried out whole-genome sequencing to identify single-nucleotide polymorphisms. We found no geographic structure at the European scale but divergent lineages within sampling sites. Evidence for recombination was restricted to specific cryptic lineages. Lineage differentiation was supported by extensive copy-number variation. Finally, we confirmed heterothallism with a single MAT1 idiomorph per genome. Synteny analyses of the MAT1 locus revealed substantial rearrangements and a pseudogene of the opposite MAT1 idiomorph. Our study provides the first evidence for substantial genome-wide structural variation, lineage-specific recombination and low continent-wide genetic differentiation in C. geophilum. Our study provides a foundation for targeted analyses of intra-specific functional variation in this major symbiosis.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). Joint Genome Institute

Sponsoring Organization:: European Regional Development Fund; French National Agency of Research (ANR); Network of Excellence Evoltree; USDOE Office of Science (SC); USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1904114

Journal Information:: Environmental Microbiology, Journal Name: Environmental Microbiology Journal Issue: 11 Vol. 23; ISSN 1462-2912

Publisher:: WileyCopyright Statement

Country of Publication:: United States

Language:: English

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