The methylome of the model arbuscular mycorrhizal fungus, Rhizophagus irregularis, shares characteristics with early diverging fungi and Dikarya

Anurag Chaturvedi,Natalia Gasilova,Laure Menin,Chanz Robbins,Ian R Sanders,Joaquim Cruz Corella,Anita Loha,Soon-Jae Lee,Frédéric G Masclaux

doi:10.1038/s42003-021-02414-5

Abstract

Early-diverging fungi (EDF) are distinct from Dikarya and other eukaryotes, exhibiting high N6-methyldeoxyadenine (6mA) contents, rather than 5-methylcytosine (5mC). As plants transitioned to land the EDF sub-phylum, arbuscular mycorrhizal fungi (AMF; Glomeromycotina) evolved a symbiotic lifestyle with 80% of plant species worldwide. Here we show that these fungi exhibit 5mC and 6mA methylation characteristics that jointly set them apart from other fungi. The model AMF, R. irregularis, evolved very high levels of 5mC and greatly reduced levels of 6mA. However, unlike the Dikarya, 6mA in AMF occurs at symmetrical ApT motifs in genes and is associated with their transcription. 6mA is heterogeneously distributed among nuclei in these coenocytic fungi suggesting functional differences among nuclei. While far fewer genes are regulated by 6mA in the AMF genome than in EDF, most strikingly, 6mA methylation has been specifically retained in genes implicated in components of phosphate regulation; the quintessential hallmark defining this globally important symbiosis.

Highlights

Early-diverging fungi (EDF) are distinct from Dikarya and other eukaryotes, exhibiting high N6-methyldeoxyadenine (6mA) contents, rather than 5-methylcytosine (5mC)
We found that EDF, including arbuscular mycorrhizal fungi (AMF), had a larger set of MT-A70 family proteins compared with Dikarya
We show that R. globosum harbors a distinctively short AMT1 homolog (Supplementary Fig. S8), and no AMT1 homolog was found in C. anguillulae, which is likely why this species has almost no symmetric 6mA methylation

Summary

Introduction

Early-diverging fungi (EDF) are distinct from Dikarya and other eukaryotes, exhibiting high N6-methyldeoxyadenine (6mA) contents, rather than 5-methylcytosine (5mC). While far fewer genes are regulated by 6mA in the AMF genome than in EDF, most strikingly, 6mA methylation has been retained in genes implicated in components of phosphate regulation; the quintessential hallmark defining this globally important symbiosis Their methylation patterns are mostly distinct from the two later diverging fungal phyla making up the Dikarya, as well as most other eukaryotes, as they exhibit high levels of N6-methyldeoxyadenine (6mA) and very low levels of 5methylcytosine (5mC)[1]. While phylogenetic studies clearly place AMF in the Mucoromycota clade of EDF6, they share some lifestyle and genomic features with the Dikarya Clonal offspring of homokaryon R. irregularis, which are genetically identical, induce large differences in cassava growth; pointing strongly to the role of epigenetic variation in symbiotic effects of these fungi[15]. Because these fungi have haploid nuclei[7], singlemolecule sequencing revealing variation within a dikaryon represents variation between the two nucleus genotypes

Methods

Results

Conclusion