Evolution of Aspergillus oryzae before and after domestication inferred by large-scale comparative genomic analysis
Naoki Watarai, Nozomi Yamamoto, Kazunori Sawada, Takuji Yamada
Department of Life Science and Technology, Tokyo Institute of Technology, 2-12-1, Ookayama, Meguro-ku, Tokyo 152-8550, Japan
Gurunavi, Inc., Toho Hibiya Building, 1-2-2 Yurakucho, Chiyoda-ku, Tokyo 100-0006, Japan

# File Description

|- GFF
  |- ${strain_ID}.gff
|- OrthoFinder_Results
  |- Orthogroups.csv (raw result of OrthoFinder v2.2.6 with "proteins_used_for_OrthoFinder.tgz")
  |- Orthogroups.csv.BUSCO96.csv (only BUSCO>96 strains)
  |- Orthogroups_UnassignedGenes.csv (unclustered single genes)
|- ortholog_exon_intron_sequences.tgz
  |- ${OG_ID}.fna (exon and intron-concatenated nucleotide sequences for BUSCO>96 strains)
  |- ${OG_ID}.fna.revised.cds.fna (ORF-aligned coding-sequences, frame-shifted or nonsense mutation allowed)
|- proteins_used_for_OrthoFinder.tgz
  |- ${strain_ID}.faa (raw protein sequences predicted by EVidenceModeler v1.1.1, complete genes only)
|- RPS_representative.fasta (Orthogroups representative protein sequences after ORF-revised)
|- RPS_representative.fasta.interpro (TSV result of InterProScan v5.28-67.0)
|- scaffolds
  |- ${strain_ID} (Gap-closed scaffolds by Platanus v1.2.4)
|- strain_list.txt (File_name(strain_ID) vs. strain_name/accession_number etc.)
|- strain_metadata.tsv (File_name vs. species/clade/industrial_usage/provider(koji manufacturer))