## 2 Materials and Methods
### Identification of Fungal Isolates Colonizing American Cranberry Plants  
The fungi isolated from roots, leaves, and fruits were identified by analyzing one of the following DNA taxonomic markers: internal transcribed spacer 1 with the 5.8S gene and internal transcribed spacer 2 (ITS), RNA polymerase II subunit B (RPB2), or translation elongation factor 1 alpha (_TEF_-1\(\alpha\)). The ITS region was used as the primary taxonomic marker to identify the isolates tested. The secondary marker genes _RPB2_ and _TEF_-1\(\alpha\) were used for isolates for which the ITS region showed 100% similarity to strains of more species. For isolates of the genus _Trichoderma_, the _TEF_-1\(\alpha\) gene was selected as a secondary marker, while for the genera _Penicillium_ and _Alternaria_, it was _RPB2_. The selection criterion was the availability of more reference sequences in the NCBI database. The following primers were used: ITS1F (5\({}^{\prime}\)-TCCGTAGGTGAACCTGCG), ITS4R (5\({}^{\prime}\)-TCCTCCGCTTATTGATATGC), and ITS5F (5\({}^{\prime}\)-GGAAGTAAAAGTCGTAACAAGG) for the ITS regions [23], TEF1-72 SF (5\({}^{\prime}\)-CATCGAGAAGTTCGAGAAGG) and TEF1 LLrev (5\({}^{\prime}\)-AACTTGCAGGAATGTG) for the _TEF_-1\(\alpha\) genes [24], and RFPB2-5F (5\({}^{\prime}\)-GAYGAYMGWATCAYTYTGG) and fRPB2-7 cR (5\({}^{\prime}\)-CCCATRGCTTGYTTRCCCAT) for the _RPB2_ genes [25]. Genomic DNA was extracted using the Syngen Fungi DNA Mini Kit according to the manufacturer's instructions (Syngen Biotech, Wroclaw, Poland).  
The polymerase chain reaction (PCR) mixture contained 4 mL of 5\(\times\) HOT FIREPol Blend Master Mix with 7.5 mM MgCl\({}_{2}\) (Solis BioDyne, Tartu, Estonia), 5 pmol \(\mu\)L\({}^{-1}\) of forward and reverse primers, and from 1.0 to 10 ng \(\mu\)L\({}^{-1}\) of genomic DNA in a total volume of 20 \(\mu\)L.  
The amplification was carried out under the following conditions: initial DNA denaturation and polymerase activation at 95 \({}^{\circ}\)C for 15 min, followed by 29 cycles of denaturation at 95 \({}^{\circ}\)C for 20 s, annealing at 55 \({}^{\circ}\)C for 30 s (for the pair of primers ITS1F--ITS4R), at 58 \({}^{\circ}\)C for 30 s (for ITS5F--ITS4R and TEF1-728F--TEF1-LLR), and at 51 \({}^{\circ}\)C for 30 s (for RPB2-5F--RPB2-7 cR), elongation at 72 \({}^{\circ}\)C for 60 s (for ITS1F--ITS4R and ITS5F--ITS4R), for 30 s (for ITS3F and ITS4R), for 90 s (for TEF1-728F--TEF1-LLR and RPB2-5F--RPB2-7 cR), and final elongation at 72 \({}^{\circ}\)C for 10 min. The effectiveness of PCR was verified using a 1.2% agarose electrophoresis gel with ethidium bromide. The products obtained were purified using the Syngen Gel/PCR Mini Kit (Syngen Biotech, Poland) following the manufacturer's instructions and, then, used as a template for the sequencing reaction, which was carried out by Genomed S.A. in Warszawa, Poland.  
Single reads were aligned using the DNAStar software (version 9.1) package (DNAStar Lasergene, Inc., Madison, WI, USA). The experimental taxonomic nucleotide databases of the National Center for Biotechnology Information (NCBI) were used to compare the isolate consensus sequences with the sequences of species-type strains deposited in the NCBI using the Basic Local Alignment Search Tool (BLAST). The taxonomic position of the isolates and the percent identity were determined by pairwise sequence alignment based on BLAST. These results were then verified by building phylogenetic trees [26] using ClustalW in MegAlign DNAStar software (version 9.1) (DNAStar Lasergene, USA) and the maximum likelihood calculation algorithm. The reliability of the tree was assessed by performing bootstrap analyses of 1000 resamples. The results of the phylogenetic analysis are presented in figures. The names of the isolates tested and the most similar reference strains are highlighted in bold font.