In-depth Phylogenomic Analysis of Arbuscular Mycorrhizal Fungi Based on a Comprehensive Set of de novo Genome Assemblies

Abstract

Morphological characters and nuclear ribosomal DNA (rDNA) phylogenies have so far been the basis of the current classifications of arbuscular mycorrhizal (AM) fungi. Improved understanding of the evolutionary history of AM fungi requires extensive ortholog sampling and analyses of genome and transcriptome data from a wide range of taxa. To circumvent the need for axenic culturing of AM fungi we gathered and combined genomic data from single nuclei to generate de novo genome assemblies covering seven families of AM fungi. We successfully sequenced the genomes of 15 AM fungal species for which genome data was not previously available. Comparative analysis of the previously published Rhizophagus irregularis DAOM197198 assembly confirm that our novel workflow generates genome assemblies suitable for phylogenomic analysis. Predicted genes of our assemblies, together with published protein sequences of AM fungi and their sister clades, were used for phylogenomic analyses. We evaluated the phylogenetic placement of Glomeromycota in relation to its sister phyla (Mucoromycota and Mortierellomycota), and found no support to reject a polytomy. Finally, we explored the phylogenetic relationships within Glomeromycota. Our results support family level classification from previous phylogenetic studies, and the polyphyly of the order Glomerales with Claroideoglomeraceae as the sister group to Glomeraceae and Diversisporales.

Early branching arbuscular mycorrhizal fungus Paraglomus occultum carries a small and repeat-poor genome compared to relatives in the Glomeromycotina

“…These analyses fully support the monophyly of Glomeromycotina and its close relationship with Mortierellomycotina within the phylum Mucoromycota [3, 56]. Remarkably, in support of rRNA-based phylogenies [57, 58], but in minor disagreement with recent protein-code-based work [5, 16, 18], our analyses place P. occultum as the earliest lineage within the Glomeromycotina phylogeny [5, 16, 18]. Furthermore, our analyses place Claroideoglomus claroideum ( Claroideoglomus is a genus that is notoriously difficult to assess phylogenetically) within Diversisporales, while other studies placed this genus either as a sister clade to Diversisporales/Glomerales [16, 18] or as a member of Glomerales [57, 58].…”

“…the sister clade of Glomeromycotina -than to most AMF species. These findings are supported by busco values indicating that the P. occultum genome space is largely sampled, and by reports of virtually identical results obtained on two members of the Paraglomerales (P. occultum and P. brasilianum) using independent approaches [18].…”

“…S2, File S7). By comparing our data with genome size and repeat estimates recently obtained from other early AMF taxa, including another member of Paraglomerales ( P. brasilianum ) [18], we found that genome size in AMF significantly correlates with repeat content in the Glomeromycotina ().…”

“…The reduced genome size and repeat content we observed is also validated by assembly sizes obtained by others on the same species and Paraglomus brasilianum using independent approaches -i.e. single nucleus sequencing (49 Mb in the work by Montoliu-Nerin et al [18] vs 44 Mb for this study).…”

“…These rRNA-based analyses supported the existence of four AMF orders – Diversisporales, Glomerales, Archaeosporales and Paraglomerales – and in these the Paraglomerales represent the earliest lineage [61]. In recent years, the advent of new sequencing methods generated protein-encoding sequence data from poorly studied lineages, and its use in phylogenomics produced a different phylogenetic scenario in which the Paraglomerales group is in a clade that contains members of the Archaeosporales ( Ambispora and Geosiphon ) [5, 18, 23, 24].…”