Inclusion of database outgroups improves accuracy of fungal meta-amplicon taxonomic assignments

Rawson, C.; Zahn, G. L.

doi:10.1101/2022.11.21.517387

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bioRxiv · 10.1101/2022.11.21.517387

Inclusion of database outgroups improves accuracy of fungal meta-amplicon taxonomic assignments

Rawson, C.·Zahn, G. L.

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Abstract

Meta-amplicon studies of fungal communities rely on curated databases for assigning taxonomy. Any host or other non-fungal environmental sequences that are amplified during PCR are inherently assigned taxonomy by these same databases, possibly leading to ambiguous non-fungal amplicons being assigned to fungal taxa. Here, we investigated the effects of including non-fungal outgroups in a fungal taxonomic database to aid in detecting and removing these non-target amplicons. We processed 15 publicly available fungal meta-amplicon data sets and discovered that roughly 40% of the reads from these studies were not fungal, though they were assigned as Fungus sp. when using a database without non-fungal outgroups. We discuss implications for meta-amplicon studies and recommend assigning taxonomy using a database with outgroups to better detect these non-fungal amplicons.

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Rawson, C., Zahn, G. L.. 2022-11-24. Inclusion of database outgroups improves accuracy of fungal meta-amplicon taxonomic assignments. https://doi.org/10.1101/2022.11.21.517387

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