Investigating unexplained genetic variation and its expression in the arbuscular mycorrhizal fungus Rhizophagus irregularis: A comparison of whole genome and RAD sequencing data

Abstract

Arbuscular mycorrhizal fungi (AMF) are important symbionts of plants. Recently, studies of the AMF Rhizophagus irregularis recorded within-isolate genetic variation that does not completely match the proposed homokaryon or heterokaryon state (where heterokaryons comprise a population of two distinct nucleus genotypes). We re-analysed published data showing that bi-allelic sites (and their frequencies), detected in proposed homo- and heterokaryote R. irregularis isolates, were similar across independent studies using different techniques. This indicated that observed within-fungus genetic variation was not an artefact of sequencing and that such within- fungus genetic variation possibly exists. We then looked to see if bi-allelic transcripts from three R. irregularis isolates matched those observed in the genome as this would give a strong indication of whether bi-allelic sites recorded in the genome were reliable variants. In putative homokaryon isolates, very few bi-allelic transcripts matched those in the genome. In a putative heterokaryon, a large number of bi-allelic transcripts matched those in the genome. Bi-allelic transcripts also occurred in the same frequency in the putative heterokaryon as predicted from allele frequency in the genome. Our results indicate that while within-fungus genome variation in putative homokaryon and heterokaryon AMF was highly similar in 2 independent studies, there was little support that this variation is transcribed in homokaryons. In contrast, within-fungus variation thought to be segregated among two nucleus genotypes in a heterokaryon isolate was indeed transcribed in a way that is proportional to that seen in the genome.

Generation of unequal nuclear genotype proportions in Rhizophagus irregularis progeny causes allelic imbalance in gene transcription

“…Thus, estimating the frequency of the two alleles can serve as a proxy for the relative abundance of both nuclear genotypes in a dikaryon. It is true that some biallelic sites were still detected in ddRADseq and whole‐genome sequencing of homokaryons (Wyss et al ., 2016; Chen et al ., 2018b; Savary et al ., 2018b; Masclaux et al ., 2019). However, these loci are very few, located in problematic regions of the assembly, and seem to have no discernible functional consequence (Masclaux et al ., 2019).…”

Host identity influences nuclear dynamics in arbuscular mycorrhizal fungi

“…Host-driven genotype selection based on their growth environment is known in other fungi, such as in the dikaryotic plant pathogen Mucor piriformis, where ratios in favor of one mating type are linked to virulence, 33 and in the non-pathogenic ascomycetes Penicillium cyclopium and Neurospora crassa. 25,26 Our findings on four dikaryotic strains of R. irregularis indicate that similar mechanisms probably affect these prominent multinucleate plant symbionts, as we found strains carrying nuclear instability suddenly producing balanced nuclear ratios upon Please cite this article in press as: Kokkoris et al, Host identity influences nuclear dynamics in arbuscular mycorrhizal fungi, Current Biology (2021), https://doi.org/10.1016/j.cub.2021.01.035 Report host switch and others reverting relative nuclear abundance in presence of a different host.…”

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

“…This variation is considered biologically important as it leads to significant differences in fungal quantitative growth traits, P uptake and transfer to plants, and plant productivity 15 , 19 , 23 , 24 . However, some R. irregularis isolates are coenocytic homokaryons, harboring multiple identical haploid nuclei, whereas others are coenocytic dikaryons, harboring a population of two haploid nucleus genotypes 7 , 8 , 25 . Clonal offspring of R. irregularis dikaryons have been shown to enormously alter the growth of rice by up to fivefold and cassava by up to threefold 15 , 26 .…”