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Rhizophagus irregularis
Image credit : Jeanne Ropars

Within the framework of the Mycorrhizal Genomics Initiative (MGI), we are sequencing a phylogenetically and ecologically diverse suite of mycorrhizal fungi (Glomeromycota, Basidiomycota and Ascomycota), which include the major clades of symbiotic species associating with plants. Analyses of these genomes will provide insight into the diversity of mechanisms for the mycorrhizal symbiosis, including arbuscular, ericoid-, orchid- and ectomycorrhizal associations.

Intra-specific genome and transcriptome diversity in the Arbuscular Mycorrhizal Rhizophagus irregularis

Arbuscular Mycorrhizal Fungi (AMF) are ubiquitous obligate symbionts that form symbiotic associations with the roots of most land plants. The positive ecological impact of AMF has attracted attention and investment from the agricultural industry with companies specializing in their production as organic means to improve crop yield and boost plant diversity. Intra-specific variation in AMF plays a pivotal role in the establishment and success of the mycorrhizal symbiosis – i.e. some genotypes enable one plant to grow better than others – yet, our current knowledge on how genomic diversity affects aspects of AMF biology are still scarce. To date, the high inter-isolate genetic variability in AMF has been suggested to result mainly from structural genomic changes among strains, including copy number variation (CNV), deletions, and insertions (indels) rather than an over-accumulation of nucleotide substitutions. However, the extent of these changes across the genome, and how they affect the function of AMF genes are facets that are not yet understood.

The goal of this sequencing project is to acquire long-awaited information on the extent of genome diversity present both within and between members of the same species. It aims to address unresolved question about these symbionts. What is the extent of genome diversity/plasticity in AMF and does it resemble that found in fungal plant pathogens? Does diversity affect particular AMF genes, or is it a more stochastic process? Does genome plasticity also affect the transcriptome of AMF strains? Which genes evolve more rapidly from selective pressures created by their hosts and the surrounding environment? To answer these questions, a genome and transcriptome-wide analysis of molecular variation has been carried out on five distinct isolates of the model AMF Rhizophagus irregularis, the only AMF species with an available reference genome. These have been propagated under axenic conditions in the Corradi lab (strains A1, A4, A5, B3, C2), and all belong to one population isolated from Switzerland.

The MGI is a large collaborative effort led by Francis Martin (INRA) aiming for master publication(s) describing the evolution of the mycorrhizal symbioses. Researchers who wish to publish analyses using data from unpublished MGI genomes are respectfully required to contact the PIs and JGI to avoid potential conflicts on data use and coordinate other publications with the MGI master paper(s).

Genome Reference(s)