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Additional file 1: Figure S1. Schematic overview of the directory structure required for the WASP pre-processing workflow. The structure can be obtained from the git repository. Users only have to provide the reference genome FASTA file and the reference genome annotation GTF file in the Reference directory as well the raw FASTQ read files in the Samples directory.

Additional file 1: Figure S1: Genomic DNA from Fusarium metavorans FW16.1 (DSM105788) was isolated using the CTAB method and 5 μL was mixed with 6 × loading buffer (0.25% (w/v) xylene cyanol, 0.25% (w/v) bromophenol blue, 30% (v/v) glycerol) and separated by 0.8% (w/v) agarose gel electrophoresis in Tris–borate EDTA (TBE) buffer at 80 V for 60 min, with the GeneRuler 1 kb Plus DNA Ladder (Thermo Fisher Scientific) as a marker. The DNA was stained with 1% ethidium bromide for 15 min and observed on a UV transilluminator (SynGene Genius, BioImaging System). Figure S2: Specific CMCase activity of the supernatants against high-viscosity CMC over time in YPD medium. Figure S3: Specific CMCase activity of the supernatants using different synthetic nutrient sources. Figure S4: Enzymatic activities for polygalacturonase (A), laminarinase (B), CMCase (C) and xylanase (D). Table S1: CMCase activity of 48 fungal strains. Table S2: CAZyme analysis of fungal isolate FW16.1 and other fungal species. The coding regions were compared with the CAZyme database (Cantarel et al. 2009; Lombard et al. 2014). Table S3: Proteins of the fungal isolate FW16.1 induced on different synthetic and artificial cellulose and biomass substrates (maize leaves (MZ) or sugar cane bagasse (SCB)). The proteins were separated by SDS-PAGE followed by in-gel tryptic digestion and LC–MS/MS. The accession number, description, coverage (%), number of peptides (# peptides), peptide-to-spectrum matches (# PSMs), molecular weight in kDa (MW [kDa]), the calculated isoelectric point (calc. pI), Score Sequest HT and number of Peptides Sequest HT (# Peptides Sequest HT) were compared with the automated translation of the genome of the fungal isolate Fusarium metavorans DSM105788. BLASTP annotations and cellular functions are also shown. Table S4: Functional prediction of the CAZymes found on different synthetic and artificial cellulose and biomass substrates. Table S5: Quantity of protein applied in the saturation curve experiments.