Stochastic nuclear organization and host-dependent allele contribution in Rhizophagus irregularis

Abstract

Background 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. Results 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 dikaryote-like R. irregularis C3 isolate and the effect of different host plants on its genetic variation. Our analyses reveal that parallel spore and root culture batches can have widely variable ratios of two main genotypes in C3. Additionally, numerous polymorphisms were found with frequencies that deviated significantly from the general genotype ratio, indicating a diverse population of slightly different nucleotypes. Changing host plants did not show consistent host effects on nucleotype ratio’s after multiple rounds of subculturing. Instead, we found a major effect of host plant-identity on allele-specific expression in C3. Conclusion Our analyses indicate a highly dynamic/variable genetic organization in different isolates of R. irregularis. Seemingly random fluctuations in nucleotype ratio’s upon spore formation, recombination events, high variability of non-tandemly repeated rDNA sequences and host-dependent allele expression all add levels of variation that may contribute to the evolutionary success of these widespread symbionts.

Detection of rare variants among nuclei populating the arbuscular mycorrhizal fungal model species Rhizophagus irregularis DAOM197198

“…It has also been demonstrated that rare variants potentially occurring in only a small fraction of all nuclei of the multinucleate R. irregularis are not easily detected ( Masclaux et al . 2019 ; van Creij et al . 2023 ).…”

“…2021 ). It was also recently demonstrated that progeny spores of the R. irregularis C3 strain can undergo random loss of genetic variation compared to their parental single spore lines even when cultured under the same conditions ( van Creij et al . 2023 ).…”

“…2023 ). Thus, the genetic composition of a single spore may not fully represent the entire genetic variation of the organism ( van Creij et al . 2023 ).…”

“…However, the stringent hard-filtering criteria did not confound their observations of signatures of potential recombination events ( Chen et al . 2020 ; van Creij et al . 2023 ).…”

“…2020 ), we concur that genomes of AM fungal strains are best understood as populations of asexually reproducing haploid nuclei ( Manley et al . 2023 ; van Creij et al . 2023 ).…”