Abstract
Evidence for the existence of dikaryote-like strains, low nuclear sequence diversity and inter-nuclear recombination in arbuscular mycorrhizal fungi has been recently reported based on single nucleus sequencing data. Here, we aimed to support evidence of inter-nuclear recombination using an approach that filters SNP calls more conservatively, keeping only positions that are exclusively single copy and homozygous, and with at least five reads supporting a given SNP. This methodology recovers hundreds of putative inter-nucleus recombination events across publicly available sequence data from individual nuclei. Challenges related to the acquisition and analysis of sequence data from individual nuclei are highlighted and discussed, and ways to address these issues in future studies are presented.
Highlights
Genome-based analyses have uncovered a large number of signatures of sexual reproduction in the arbuscular mycorrhizal fungi (AMF), challenging the notion that these organisms are ancient asexuals (Halary et al, 2011, 2013; Tisserant et al, 2013; Riley et al, 2014; Corradi and Brachmann, 2016; Ropars et al, 2016; Chen et al, 2018a)
This study supported the hypothesis that two genotypes co-exist in some AMF isolates, and confirmed that overall nuclear genetic diversity is low in these organisms
Because conservative methods can be applied to study larger datasets, we implemented it to a larger dataset – i.e., 1000 contiguous, as opposed to 100 analyzed in Chen et al (2018b) - to gather a better view of recombination events in AMF dikaryons
Summary
Genome-based analyses have uncovered a large number of signatures of sexual reproduction in the arbuscular mycorrhizal fungi (AMF), challenging the notion that these organisms are ancient asexuals (Halary et al, 2011, 2013; Tisserant et al, 2013; Riley et al, 2014; Corradi and Brachmann, 2016; Ropars et al, 2016; Chen et al, 2018a). The nuclei of dikaryotic AMF isolates each carry one of two divergent regions that resemble the mating-type (MAT) loci of sexual fungi – i.e., putative idiomorphs. To confirm the existence of low nuclear diversity and dikaryotic stages in AMF, as well as to test whether recombination occurs among co-existing nuclei, a recent study sequenced 86 single nuclei from seven AMF isolates (Chen et al, 2018b). This study supported the hypothesis that two genotypes co-exist in some AMF isolates, and confirmed that overall nuclear genetic diversity is low in these organisms. It showed evidence that rare inter-nucleus recombination events can be found in dikaryotic AMF strains (Chen et al, 2018b)
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