In mycobiome studies, most primers currently designed and promoted as broadly-fungal specific exclude the deep-branching and evolutionarily ancient fungal or fungal-like organisms in specific phyla (e.g. Chytridiomycota, Glomeromycota and Oomycota). In turn, these taxa must be targeted by group-specific (e.g. Glomeromycota) or broadly eukaryotic primers (e.g. Chytridiocota, Oomycota) to generate amplicons that sufficiently capture such taxonomic groups (Geisen et al. 2019; Lucking et al. 2020; Řezáčová et al. 2019; Stockinger et al. 2010; Wurzbacher et al. 2016). Previous efforts have applied universal fungal primers to analyze arbuscular mycorrhizal fungal communities in both root and soil samples, and reveal similar alpha-diversity estimates using such an approach as compared to sequencing amplicons generated with taxon-specific primers, albeit with much shallower depth. This is because the representation of Glomeromycota in the amplicons generated by supposedly fungal-specific primers is often suppressed as compared to Asco- and Basidiomycota, particularly when working with soil samples (Berruti et al. 2017).
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