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.
Highlights
After whole genome amplification (WGA) with multiple displacement amplification (MDA) on the sorted nuclei, samples from the remaining 29 isolates were screened by PCR amplification of the ribosomal DNA (rDNA) barcode region for presence of DNA of fungal and bacterial origin
In the current study we present a considerable increase in the number of Arbuscular mycorrhizal (AM) fungal genome assemblies available, thanks to the development of single nuclei sequencing and de novo assembling in AM fungi that we recently developed
As demonstrated for Rh. irregularis, variation in sequencing depth and coverage of single nuclei due to MDA, was accounted for in our de novo genome assemblies that provide a satisfactory representation of the genome content even when the assemblies generated are fragmented
Summary
Arbuscular mycorrhizal (AM) fungi are an ecologically important group of fungi that form ubiquitous associations with plants, establishing symbiosis with up to 80% of land plant species (Parniske, 2008; Smith and Read, 2010). Available literature identify that all AM fungi form a monophyletic lineage within the fungal kingdom This lineage is taxonomically classified either as a phylum, Glomeromycota (Schüβler et al, 2001; Hibbett et al, 2007; Schüßler and Walker, 2010; Tedersoo et al, 2018), or as the sub-phylum Glomeromycotina, which together with Mortierellomycotina and Mucoromycotina, make up the phylum Mucoromycota (Spatafora et al, 2016; James et al, 2020; Li et al, 2021). The current consensus classification of AM-fungal species into genera and families was established by Redecker et al in 2013, when systematists with long experience in the biology and taxonomy of AM fungi joined forces to integrate morphological and molecular phylogenetic information to generate a meaningful classification that reflects evolutionary relationships (Redecker et al, 2013). Around 300 species of AM fungi are currently described and classified into 33 genera, twelve families and four orders (Redecker et al, 2013; Wijayawardene et al, 2018)
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