Database Construction

Sequences classified as fungi (Taxonomy ID:4751) were extracted from the NCBI-nt database. Additional sequences with ambiguous taxonomic information (those whose taxonomic name included the terms “uncultured,” “environmental,” “unclassified,” or “mixed”) were excluded. From these sequences, the ITS1 region was identified between the ITS1-F (5′-CTTGGTCATTTAGAGGAAGTAA-3′) and ITS2 (5′-GCATCGATGAAGAACGCAGC-3′) sequences using cutadapt-1.7.1 with default parameters (Martin and Marcel, 2011). Because no ITS1 sequences were identified for Rhodosporidium babjevae. Acremonium alternatum. Penicillium digitatum. Mucor ramosissimus, or Rhizopus oryzae in the curated NCBI-nt database, we manually added these sequences to our database. The resulting sequences were converted into a format that was suitable for the Ribosomal Database Project (RDP) Classifier (Wang et al., 2007), and this was used as the database nt-Fungi-ITS1 (ntF-ITS1) for mycobiota analysis. Sequence extraction and format conversion were conducted with a Ruby script. The ntF-ITS1 database can be downloaded from our website¹.