PRJNA565592
Amplicon sequencing of fungal mock community
The goal of this project was to execute a selected pipeline and determine if the MinION nanopore sequencer could accurately identify a broad diversity of fungal organisms (e.g., something that may be similar to what was extracted from an environmental sample). DNA was extracted from a diversity of fungal sporocarps and cultures belonging to Basidiomycota, Ascomycota, and Mucoromycotina. The taxa were pooled together in three mock communities (Mock A, Mock B, Mock C). Mock A had an even ratio of all taxa, which were combined at .028 ng/µl each. Mock B and Mock C had selected species staggered at a 1:10 ratio. The pipeline utilized Albacore, NanoFilt, MAFFT, PHYLIP, and mothur. Subsequently, custom python scripts were used calculate consensus sequences from OTU alignments. This approach identified all mock community members to species level in the even mock community. When taxa were represented at a lower ratio, they either decreased substantially in relative abundance or were not recovered. The results demonstrate that the MinION holds potential as a pragmatic alternative for identifying a diversity of fungi from environmental samples, when rare taxa are not of concern.