Comparative genomics and transcriptomics depict ericoid mycorrhizal fungi as versatile saprotrophs and plant mutualists

• DOI: 10.1111/nph.14974
• Publication Date: 2018-01-10T04:25:47Z
• Authors: Elena Martino; Emmanuelle Morin; Gwen‐Aëlle Grelet; Alan Kuo; Annegret Kohler; Stefania Daghino; Kerrie W. Barry; Nicolas Cichocki; Alicia Clum; Rhyan B. Dockter; Matthieu Hainaut; Rita C. Kuo; Kurt LaButti; Björn D. Lindahl; Erika A. Lindquist; Anna Lipzen; Hassine‐Radhouane...; Jon Magnuson; Claude Murat; Robin A. Ohm; Steven W. Singer; Joseph W. Spatafora; Mei Wang; Claire Veneault‐F...; Bernard Henrissat; Igor V. Grigoriev; Francis M. Martin; Silvia Perotto
• Keywords: 0301 basic medicine; 570; Leotiomycetes; [SDV]Life Sciences [q-bio]; Plant Biology & Botany; Genes, Fungal; Secondary Metabolism; comparative genomics; Microbiology; Ecological applications; Substrate Specificity; transcriptomics; 03 medical and health sciences; ericoid mycorrhizal fungi; Gene Expression Regulation, Fungal; Mycorrhizae; Taverne; Genetics; Symbiosis; Conserved Sequence; Phylogeny; Plant biology; 2. Zero hunger; Ecology; Agricultural and Veterinary Sciences; Fungi; 500; Genomics; comparative genomics, Ericaceae, ericoid mycorrhizal fungi, Leotiomycetes, transcriptomics; Biological Sciences; Plants; 15. Life on land; Up-Regulation; Fungal; Gene Expression Regulation; Genes; Climate change impacts and adaptation; Ericaceae; Transcriptome; Responsible Consumption and Production; Biotechnology

Summary

Some soil fungi in the Leotiomycetes form ericoid mycorrhizal (ERM) symbioses with Ericaceae. In the harsh habitats in which they occur, ERM plant survival relies on nutrient mobilization from soil organic matter (SOM) by their fungal partners. The characterization of the fungal genetic machinery underpinning both the symbiotic lifestyle and SOM degradation is needed to understand ERM symbiosis functioning and evolution, and its impact on soil carbon (C) turnover. We sequenced the genomes of the ERM fungi Meliniomyces bicolor, M. variabilis, Oidiodendron maius and Rhizoscyphus ericae, and compared their gene repertoires with those of fungi with different lifestyles (ecto‐ and orchid mycorrhiza, endophytes, saprotrophs, pathogens). We also identified fungal transcripts induced in symbiosis. The ERM fungal gene contents for polysaccharide‐degrading enzymes, lipases, proteases and enzymes involved in secondary metabolism are closer to those of saprotrophs and pathogens than to those of ectomycorrhizal symbionts. The fungal genes most highly upregulated in symbiosis are those coding for fungal and plant cell wall‐degrading enzymes (CWDEs), lipases, proteases, transporters and mycorrhiza‐induced small secreted proteins (MiSSPs). The ERM fungal gene repertoire reveals a capacity for a dual saprotrophic and biotrophic lifestyle. This may reflect an incomplete transition from saprotrophy to the mycorrhizal habit, or a versatile life strategy similar to fungal endophytes.