#Additional File 1 : Genome assembly and assessment 

#Quality assessement of raw reads (412_1.fastq.gz and 412_2.fastq.gz) using FastQC v0.11.5
mkdir fastqc_out
fastqc 412_1.fastq.gz 412_2.fastq.gz -o fastqc_out

#Trimming of raw reads using Trimmomatic v0.39 
java -jar $TRIMMOMATIC PE -phred33 -threads 2 412_1.fastq.gz 412_2.fastq.gz R1_trimmed.fastq.gz R1_singles.fastq.gz R2_trimmed.fastq.gz R2_singles.fastq.gz ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:25 MINLEN:50 2>&1 | tee trimmomatic.log

cat R1_singles.fastq.gz R2_singles.fast.gz > Singles.fastq.gz

#Quality assessement of trimmed reads (R1_trimmed.fastq.gz and R2_trimmed.fastq.gz) using FastQC v0.11.5
mkdir fastqc_out
fastqc R1_trimmed.fastq.gz R2_trimmed.fastq.gz -o fastqc_out

#Genome assembly using SPAdes v3.13.0 
spades.py -t 4 -o 412_spades --pe1-1 R1_trimmed.fastq.gz --pe1-2 R2_trimmed.fastq.gz --pe1-s Singles.fastq.gz

#Filtering out contigs of <1000p using SeqKit v0.8.0
seqkit seq -m 1000 scaffolds.fasta > assembly1.1.fasta

#Assessing basic genome statistics using QUAST v5.1 
quast.py -o Quast1.1 -t 4 assembly1.1.fasta

#Assessing genome comleteness and contamination using BUSCO v4.0.6
#BUSCO was used to assess all 22 genomes, below is the R. undulata example
busco --offline -i assembly1.1.fasta --download_path /apps/busco-5.3.2/busco_downloads -l fungi_odb10 -o busco_fungi -m genome
busco --offline -i assembly1.1.fasta --download_path /apps/busco-5.3.2/busco_downloads -l ascomycota_odb10 -o busco_asco -m genome
busco --offline -i assembly1.1.fasta --download_path /apps/busco-5.3.2/busco_downloads -l bacteria_odb10 -o busco_bact -m genome