At the nexus of three kingdoms: the genome of the mycorrhizal fungus Gigaspora margarita provides insights into plant, endobacterial and fungal interactions

Abstract

As members of the plant microbiota, arbuscular mycorrhizal fungi (AMF, Glomeromycotina) symbiotically colonize plant roots. AMF also possess their own microbiota, hosting some uncultivable endobacteria. Ongoing research has revealed the genetics underlying plant responses to colonization by AMF, but the fungal side of the relationship remains in the dark. Here, we sequenced the genome of Gigaspora margarita, a member of the Gigasporaceae in an early diverging group of the Glomeromycotina. In contrast to other AMF, G. margarita may host distinct endobacterial populations and possesses the largest fungal genome so far annotated (773.104 Mbp), with more than 64% transposable elements. Other unique traits of the G. margarita genome include the expansion of genes for inorganic phosphate metabolism, the presence of genes for production of secondary metabolites and a considerable number of potential horizontal gene transfer events. The sequencing of G. margarita genome reveals the importance of its immune system, shedding light on the evolutionary pathways that allowed early diverging fungi to interact with both plants and bacteria.

Different Genetic Sources Contribute to the Small RNA Population in the Arbuscular Mycorrhizal Fungus Gigaspora margarita

“…Screening the Pfam annotation of the G. margarita proteome (Venice et al, 2019), we retrieved all the sequences containing a "Piwi" (Pfam ID: PF02171.17), an "RdRP" (Pfam ID: PF05183.12), or two "Ribonuclease_3" (Pfam ID: PF00636.26) domains, and we considered them as AGO-like, RdRp, or DCL, respectively. The whole amino acid sequences of DCL, AGOlike, and RdRp were aligned with MAFFT v7.310 (option:auto) (Katoh and Standley, 2013) together with fungal sequences analyzed in Silvestri et al (2019).…”

“…Further filtering of raw reads was performed with Bowtie (Langmead et al, 2009), by removing the reads that mapped with up to 1 mismatch to the tRNA, rRNA, snRNA, and snoRNA sequences from Rfam 12.0 database (Nawrocki et al, 2015), and those mapping with 0 mismatches to all the "ribosomal RNA" sequences present in GenBank for Mucoromycota taxonomy; we finally kept only the 18-to 35-nt long reads. Filtered reads were mapped with no mismatch with bowtie to the unmasked versions of G. margarita nuclear (Venice et al, 2019), mitochondrial (Pelin et al, 2012), CaGg (Ghignone et al, 2012), and viral (Turina et al, 2018) genomes. A set of Bash, Perl, and R scripts were used for the analysis and visualization of nucleotide length distribution, 5 -end nucleotide composition, and reads redundancy.…”

“…ShortStack v.3.8.5 (Johnson et al, 2016) was used for genome-guided sRNA-generating loci prediction and annotation on G. margarita nuclear genome (options: -mismatches 0foldsize 1000 -dicermin 18 -dicermax 35 -pad 200 -mincov 10.0rpmm). BEDTools (Quinlan and Hall, 2010) was used to compare the genomic locations of sRNA-generating loci with those of annotated protein-encoding genes and of annotated transposable elements (Venice et al, 2019). PCA on sRNAgenerating loci was performed in R with "FactoMineR" v1.42 (Lê et al, 2008) and "factoextra" v1.0.5 1 packages.…”

“…These works highlighted that the two analyzed AMF, R. irregularis and R. clarus, are equipped with a RNAi machinery characterized by 26-40 AGO-like, 3-21 RdRp, and 1-2 DCL proteins. Here we analyzed the genome of the AMF G. margarita (Venice et al, 2019) in order to define the conservation level of the RNAi-related genes in the Glomeromycotina subphylum. Keeping only one virtual transcript for each gene, we obtained a total of 11 AGO-like, 6 RdRp, and 1 DCL corresponding proteins.…”

“…The RNAi machinery and the sRNA populations in AMF have been characterized only in the model AMF species Rhizophagus irregularis (Lee et al, 2018;Silvestri et al, 2019). The availability of the full genome sequence of Gigaspora margarita (Venice et al, 2019) offered the possibility to explore how conserved are RNAi features in AMF. G. margarita is of particular interest as it belongs to Gigasporaceae, an early diverging AMF group, well separated from Glomeraceae that includes R. irregularis (Krüger et al, 2012).…”