#Additional File 4 : Gene prediction and functional annotations

#These analyses were conducted for each of the 22 genomes, R. undulata is shown as an example below.

#Gene prediction using Funannotate v1.8.15
funannotate predict -i assembly3.1.fasta --out Fun412 --species “Rhizina undulata” --strain CMW412 --name “RUND412”	--protein_evidence Rhiund1_GeneCatalog_proteins_20190327.fa --cpus 1 

#Classify predicted protiens using InterProScan v5.52-86.0
interproscan.sh -i Rhizina_undulata_CMW412.proteins.fa --outfile funannotate_folder/annotate_misc/iprscan.xml --formats xml --cpu 6

#Assign functional information using eggNOG-Mapper v2.1.11
emapper.py -i ../predict_results/Rhizina_undulata_CMW412.proteins.fa --data_dir /apps/eggnogmapper/data/ -o Egg --cpu 4

#Identify secondary metabolite clusters using AntiSmash v6.1.1
antismash --taxon fungi --output-dir AntiSmash --genefinding-tool none --cpus 5	/predict_results/Rhizina_undulata_CMW412.gbk

#Identify transmembrane domains and signal peptides using Phobius v1.01
phobius.pl -short predict_results/Rhizina_undulata_CMW412.proteins.fa > phobius.results.txt

#Functionally annotate predicted genes using Funannotate v1.8.15
funannotate annotate -i FUN412 --iprscan FUN412/annotate_misc/iprscan.xml --antismash FUN412/annotate_misc/Rhizina_undulata_CMW412.gbk --eggnog FUN412/annotate_misc/Egg.emapper.annotations --cpus 5 --sbt FUN412/annotate_misc/412.sbt

#Compare genomes using Funannotate v1.8.15
funannotate compare --input AIMM ANIG MIMP MSEX MCON MSNY TBOU TCLA TNIV PECH KPFE THYB GCAR PDOM POMP SBRU WMIK ../FUN412 CVEN2 TBRU2 TMEL2 TBOR2 TMAG2 OOLI