Arbuscular mycorrhizal fungi (AMF) are part of the most widespread fungal-plant symbiosis. They colonize at least 80% of plant species, promote plant growth and plant diversity. These fungi are multinucleated and contain either one or two haploid nuclear genotypes (monokaryon and dikaryon) identified by the alleles at a putative mating-type locus. This taxon has been considered as an ancient asexual scandal because of the lack of observable sexual structures. Despite identification of a putative mating-type locus and functional activation of genes related to mating when two isolates co-exist, it remains unknown if the AMF life cycle involves a sexual or parasexual stage. We used publicly available genome sequences to test if Rhizophagus irregularis dikaryon genomes display signatures of sexual reproduction in the form of reciprocal recombination patterns, or if they display exclusively signatures of parasexual reproduction involving gene conversion. We used short-read and long-read sequence data to identify nucleus-specific alleles within dikaryons and then compared them to orthologous gene sequences from related monokaryon isolates displaying the same putative MAT-types as the dikaryon. We observed that the two nucleus-specific alleles of the dikaryon A5 are more related to the homolog sequences of monokaryon isolates displaying the same putative MAT-type than between each other. We also observed that these nucleus-specific alleles displayed reciprocal recombination signatures. These results confirm that dikaryon and monokaryon isolates displaying the same putative MAT-type are related in their life-cycle. These results suggest that a genetic exchange mechanism, involving reciprocal recombination in dikaryon genomes, allows AMF to generate genetic diversity.
Arbuscular mycorrhizal fungi (AMF) are part of the most widespread fungal-plant symbiosis. They colonize at least 80% of plant species, promote plant growth and plant diversity. These fungi are multinucleated and display either one or two nucleus genotypes (monokaryon and dikaryon) determined by a putative mating-type locus. This taxon has been considered as an ancient asexual scandal because of the lack of observable sexual structures. Despite the identification of a putative mating-type (MAT-type) locus and the functional activation of genes related to mating when two isolates co-exist, it is still unknown if AMF display a sexual or a parasexual life cycle. To test if AMF genomes display signatures of a sexual life-cycle involving the putative MAT-locus, we used publicly available genome sequences to test if recombining nucleotype-specific haplotypes could be identified using short-read Illumina sequences. We identified nucleus genotype-specific haplotypes within dikaryons and compared them to orthologous gene sequences from related monokaryon isolates displaying similar putative MAT-types. We show that haplotypes within a dikaryon isolate are more similar to homologue sequences of isolates having the same MAT-type than among them. We demonstrate that these genotype-specific haplotypes are recombinant, and are not consistently most similar to the monokaryon isolate sharing the same mating-type allele. These results are consistent with a sexual origin of the dikaryon rather than a parasexual origin and provides an important step to understand the life cycle of these globally important symbiotic fungi.
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