Genome-level analyses resolve an ancient lineage of symbiotic ascomycetes Author Díaz-Escandón, David Department of Biological Sciences CW 405, University of Alberta, Edmonton, AB T 6 G 2 R 3, Canada Author Tagirdzhanova, Gulnara Department of Biological Sciences CW 405, University of Alberta, Edmonton, AB T 6 G 2 R 3, Canada Author Vanderpool, Dan National Genomics Center for Wildlife and Fish Conservation, Rocky Mountain Research Station, 800 E Beckwith, Missoula, MT 59812, USA Author Allen, Carmen C. G. Department of Biological Sciences CW 405, University of Alberta, Edmonton, AB T 6 G 2 R 3, Canada Author Aptroot, André Laboratório de Botânica / Liquenologia, Instituto de Biociências Universidade Federal de Mato Grosso do Sul, Avenida Costa e Silva s / n Bairro Universitário, Campo Grande, Mato Grosso do Sul CEP 79070 - 900, Brazil Author Češka, Oluna Victoria, BC, Canada Author Hawksworth, David L. Comparative Fungal Biology, Royal Botanic Gardens, Kew, Surrey TW 9 3 DS, UK & Department of Life Sciences, The Natural History Museum, Cromwell Road, London SW 7 5 BD, UK & Jilin Agricultural University, Changchun, Jilin Province 130118, China Author Huereca, Alejandro Department of Biological Sciences CW 405, University of Alberta, Edmonton, AB T 6 G 2 R 3, Canada Author Knudsen, Kerry Czech University of Life Sciences, Faculty of Environmental Sciences, Department of Ecology, Kamýcká 129, Praha-Suchdol 165 00, Czech Republic Author Kocourková, Jana Czech University of Life Sciences, Faculty of Environmental Sciences, Department of Ecology, Kamýcká 129, Praha-Suchdol 165 00, Czech Republic Author Lücking, Robert Botanischer Garten, Freie Universität Berlin, Königin-Luise-Straße 6 - 8, 14195 Berlin, Germany Author Resl, Philipp Institute of Biology, University of Graz, Universit € atsplatz 2, 8010 Graz, Austria Author Spribille, Toby Department of Biological Sciences CW 405, University of Alberta, Edmonton, AB T 6 G 2 R 3, Canada & text Current Biology 2022 2022-11-30 30 6 1 10 http://dx.doi.org/10.1016/j.cub.2022.11.014 journal article 10.1016/j.cub.2022.11.014 7358475

Continued

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Gotree v0.4.2	Lemoine and Gascuel74	https://github.com/evolbioinfo/gotree
Funannotate v1.7.4, v1.8.1, v1.8.3, v1.8.5, v1.8.6, v1.8.8	Palmer and Stajich75	https://github.com/nextgenusfs/funannotate
RepeatMasker v4.1.0 Gene-Mark-ES v4.59_lic	Smit et al.76 Ter-Hovhannisyan et al.77	http://repeatmasker.org http://exon.gatech.edu/GeneMark/ gmes_instructions.html
Augustus v3.3.3 (within Funannotate) GlimmerHMM v3.0.4 (within Funannotate)	Stanke et al.78 Majoros et al.79	http://bioinf.uni-greifswald.de/augustus/ https://ccb.jhu.edu/software/glimmerhmm/
SNAP v2013_11_29 (within Funannotate) EVidence Modeler v1.1.1 (within Funannotate)	Korf80 Haas et al.81	https://github.com/KorfLab/SNAP https://evidencemodeler.github.io
tRNAscan-SE v1.4.0 (within Funannotate)	Lowe et al.82	http://trna.ucsc.edu/tRNAscan-SE/
InterProScan v5.48-83.0	Jones et al.83	https://github.com/ebi-pf-team/interproscan
eggnog-mapper v1.0.3	Huerta-Cepas et al.84	https://github.com/eggnogdb/eggnog-mapper
HMMER v3.1b2 (within eggnog-mapper)	HMMER	http://hmmer.org
phobius v1.0.1	Kall € et al.85	https://phobius.sbc.su.se
antiSMASH v5.0.2, v6.0.0	Blin et al.86,87	http://antismash.secondarymetabolites.org
Signalp v4.1	Nielsen88	https://services.healthtech.dtu.dk/ service.php?SignalP-4.1
Phytools	Revell89	http://www.phytools.org
Diamond v2.0.7.145 (within eggnog-mapper)	Buchfink et al.90	https://github.com/bbuchfink/diamond
Databases
NCBI Genome (for 467 genomes; Data S1C)	NCBI Genome	https://www.ncbi.nlm.nih.gov/genome/
NCBI Short Read Archive (for Dibaeis baeomyces and Graphis scripta raw reads)	NCBI SRA	https://www.ncbi.nlm.nih.gov/sra
eggNOG db v4.5.4	Huerta-Cepas et al.91	http://eggnog45.embl.de/#/app/home
PFAM db v33.1 (within Funannotate)	Mistry et al.92	https://pfam.xfam.org
dbCAN v9.0 (within Funannotate)	Yin et al.93	https://bcb.unl.edu/dbCAN2/
MEROPS db v12.0 (within Funannotate)	Rawlings et al.94	https://www.ebi.ac.uk/merops/
UniProtKB db v.2020_06 (within Funannotate)	Uniprot Consortium95	https://www.uniprot.org/help/uniprotkb
Mycobank	Mycobank	https://www.mycobank.org
Other
Scripts and code for analysis	Figshare	https://doi.org/10.6084/ m9.figshare.19558762