A draft genome sequence of the arbuscular mycorrhizal Gigaspora margarita: investigating cross-kingdom interactions

Arbuscular mycorrhizal fungi (AMF) are members of the plant microbiota, being associated with the roots of most land plants, and enhancing the host’s ability to acquire nutrients. On the other hand, they host their own microbiota (Desiro et al, 2014), since some of them possess obligate endobacteria. AMF represent therefore the hub for an interkingdom interaction between plants, fungi and bacteria (Bonfante and Desirò, 2017). The fungal endobacteria show reduced genomes and nutritional dependence on the fungal host (Ghignone et al., 2012; Torres-Cortès et al., 2015), but functional OMICs analyses suggested that their presence deeply impacts AMF host physiology (Salvioli et al., 2016; Vannini et al., 2016). While genome-scale comparisons have become a powerful tool for the reconstruction of the fungal lineage (Spatafora et al., 2017), genomics data for AMF are available only for Rhizophagus irregularis (Tisserant et al., 2013; Lin et al., 2014), that does not possess endobacteria. Here, we present a draft genome sequence of Gigaspora margarita BEG34, which hosts the endobacterium Candidatus Glomeribacter gigasporarum. The nuclear genome sequence of G. margarita is ~775Mb, almost 6 times bigger than R. irregularis. While scanning for transposable elements and centromeric/telomeric regions, we discovered that ~80% of G. margarita genome mainly contains repeated sequences ascribable to transposable elements. Preliminary approaches for gene prediction revealed a low gene density (~4 genes/100Kb on average), and allowed the identification of genomic regions with homology to known bacterial sequences. On one hand, the genome of G. margarita has size and composition features which make its description a challenging task, but on the other hand it will provide interesting clues to understand how AMF evolved, allowing some fungal isolates to harbor endosymbionts, and in the mean time to interact with the host plant.