Arbuscular mycorrhizal (AM) fungi are arguably the most important symbionts of plants, offering a range of benefits to their hosts. However, the provisioning of these benefits does not appear to be uniform among AM fungal individuals, with genetic variation between fungal symbionts having a substantial impact on plant performance. Interestingly, genetic variation has also been reported within fungal individuals, which contain millions of haploid nuclei sharing a common cytoplasm. In the model AM fungus, Rhizophagus irregularis, several isolates have been reported to be dikaryotes, containing two genetically distinct types of nuclei recognized based on their mating-type (MAT) locus identity. However, their extremely coenocytic nature and lack of a known single nucleus stage has raised questions on the origin, distribution and dynamics of this genetic variation.
Here we performed DNA and RNA sequencing at the mycelial individual, single spore and single nucleus levels to gain insight into the dynamic genetic make-up of the R. irregularis C3 isolate. This isolate is thought to be clonally related to the recently sequenced dikaryon-like A4 isolate, which both were isolated ~ 20 years ago from the same field in Switzerland. Our analyses reveal that both isolates vary considerably in their nuclear behavior. Parallel spore and root culture batches showed widely variable ratios of two main nucleotypes in C3. Additionally, numerous polymorphisms were found that deviated significantly from the distribution of the two main nucleotypes in C3. No consistent host effects on nucleotype ratio after multiple rounds of subculturing were observed. Instead, we found a major effect of host plant-identity on allele-specific expression in C3.
Our analyses indicate a much more dynamic/variable genetic organization in R. irregularis than previously assumed. Seemingly random fluctuations in nucleotype ratio’s upon spore formation, recombination events, high variability of non-tandemly repeated rDNAs and host-dependent allele specific expression all add levels of variation that may contribute to the evolutionary success of these widespread symbionts.