The draft genome of the arbuscular mycorrhizal fungus Gigaspora margarita: a niche where to search for plant and bacterial interacting traits

As obligate biotrophs colonizing the roots of most land plants, arbuscular mycorrhizal fungi (AMF) are crucial members of the rhizosphere microbiota, being able to increase plant fitness through mineral nutrition.Some AMF species are at the center of a network which involves plants, fungi and bacteria, since they possess obligate endobacteria inside their cytoplasm (Bonfante and Desirò, 2017, in press). These bacteriashow reduced genomes and nutritional dependence on the fungal host (1,2), but functional analyses based on OMICs approaches suggested that their presence deeply impacts AMF host physiology (3,4). However, genomics AMF data are available only for Rhizophagus irregularis (5,6), which does not possess endobacteria. Here, we present the draft genome sequence of Gigaspora margarita BEG34, which lives associated with the endobacterium Candidatus Glomeribacter gigasporarum. By discriminating the genomic scaffolds on the basis of their GC content, we were able to exclude the bacterial and mitochondrial sequences from the dataset, and estimated the nuclear genome size of G. margarita ~785Mb, almost 6 times bigger than R. irregularis. While scanning for transposable elements and centromeric/telomeric regions, we discoveredthat ~80% of G. margarita consists of repeated regions. Also, some nuclear scaffolds have eukaryotic GC content but show homology with bacterial sequences. Further investigations will shed light on this complex genome, offering a new tool to better understand AMF lifestyle.