Abstract
Arbuscular mycorrhizal fungi (AMF) are one of the most widespread symbionts of land plants. Our substantially improved reference genome assembly of a model AMF, Rhizophagus irregularis DAOM-181602 (total contigs = 210, contig N50 = 2.3Mbp) facilitated discovery of repetitive elements with unusual characteristics. R. irregularis has only ten to eleven copies of the complete 45S rDNA, whereas the general eukaryotic genome has tens to thousands of rDNA copies. R. irregularis rDNAs are highly heterogeneous and lack a tandem repeat structure. These findings provide evidence for the hypothesis of concerted evolution that rDNA homogeneity depends on its tandem repeat structure. RNA-seq analysis confirmed that all rDNA variants are actively transcribed. Observed rDNA/rRNA polymorphism may modulate translation by using different ribosomes depending on biotic and abiotic interactions. The non-tandem repeat structure and intragenomic heterogeneity of AMF rDNA may facilitate adaptation to a broad host range despite lacking a sexual life cycle.