Ultra-low input transcriptomics reveal the spore functional content and phylogenetic affiliations of poorly studied arbuscular mycorrhizal fungi

Abstract

Arbuscular mycorrhizal fungi (AMF) are a group of soil microorganisms that establish symbioses with the vast majority of land plants. To date, generation of AMF coding information has been limited to model genera that grow well axenically; Rhizoglomus and Gigaspora. Meanwhile, data on the functional gene repertoire of most AMF families is non-existent. Here, we provide primary large-scale transcriptome data from eight poorly studied AMF species (Acaulospora morrowiae, Diversispora versiforme, Scutellospora calospora, Racocetra castanea, Paraglomus brasilianum, Ambispora leptoticha, Claroideoglomus claroideum and Funneliformis mosseae) using ultra-low input ribonucleic acid (RNA)-seq approaches. Our analyses reveals that quiescent spores of many AMF species harbour a diverse functional diversity and solidify known evolutionary relationships within the group. Our findings demonstrate that RNA-seq data obtained from low-input RNA are reliable in comparison to conventional RNA-seq experiments. Thus, our methodology can potentially be used to deepen our understanding of fungal microbial function and phylogeny using minute amounts of RNA material.

Genome and evolution of the arbuscular mycorrhizal fungus Diversispora epigaea (formerly Glomus versiforme) and its bacterial endosymbionts

“…Spore transcriptome sequences of multiple Glomeromycotina fungi have been published recently (Beaudet et al ., ). We incorporated these data to date the divergence of AM fungi.…”

“…We incorporated these data to date the divergence of AM fungi. The Glomeromycotina is the basal lineage of Mucoromycota (Beaudet et al ., ), and the time when it diverged from its most recent ancestor was estimated to be 586 Ma (Fig. a).…”

Genome-scale phylogenetic analyses confirmOlpidiumas the closest living zoosporic fungus to the non-flagellated, terrestrial fungi

“…We sampled proteome sequences from a total of 113 species (106 fungi and seven nonfungus outgroups; Table S1) in our phylogenetic reconstruction. We employed 434 protein markers that proved useful for the inference of higher-level phylogenetic relationships among fungi 29,38 (https://github.com/1KFG/Phylogenomics_HMMs). We used the pipeline PHYling (Stajich JE; http://github.com/stajichlab/PHYling_unified) to search for the target markers in the sampled proteomes with an e-value of -20 and performed alignment for each marker.…”

Dynamic Phosphate Uptake in Arbuscular Mycorrhizal Roots Under Field Conditions

“…A recently established approach designed for single-cell genomics and transcriptomics enables more high-throughput simultaneous analysis of many AMF species to discover the potential of the expression of their specific functions. Spore-based RNA sequencings were successfully applied to obtain transcript datasets from several AMF taxa, including genetically obscure genera such as Paraglomus, Ambispora, and Diversispora (Beaudet et al, 2018), highlighting their reproduction process, translation, amino acid metabolism, or energy production (Beaudet et al, 2018). However, not only quantitative evaluation of the "existence" of AMF nucleotide sequences but also evaluation of the hidden "dynamics" of the function in the mosaic of AMF might be necessary to accurately track the functionality of mycorrhizal roots (van der Heijden and Scheublin, 2007).…”