Taxonomic allocation of sequence readings and diversity
index
The paired-end reading sequences generated from Illumina MiSeq were
processed using the software package “Quantitative Insights into
Microbial Ecology 2” (QIIME 2, v2018.6) (Caporaso et al. 2010). Briefly,
readings were demultiplexed, trimmed, filtered, and merged with the
DADA2 complement (Callahan 2016), keeping the sequences with a minimum
quality score of 25, a minimum length of 240 bp for reverse readings,
and a maximum length of 260 bp for advanced readings. Merged reads
collapsed into representative sequences or ASV. Then, ASVs were filtered
through the novo chimera using VSEARCH (Rognes et al. 2016). The
taxonomy of ASV was assigned at a 99% sequence identity based on the
UNITE v7 database (Kõljalg 2013). Non-fungal sequences were removed from
the subsequent analysis, and the ASV table was rarefied to a uniform
depth (100,000 sequences per sample) to reduce bias related to the depth
of sequencing. Taxonomy and shared files produced in QIIME 2 were
imported into R (R Core Team 2018) using the Phyloseq package (McMurdie
et al. 2013) where α and β diversity were calculated.