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

KEY RESOURCES TABLE

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Biological samples
Herbarium specimen of Watsoniomyces obsoletus used for metagenome sequencing	Herbarium ALTA	https://www.ualberta.ca/museums/ museum-collections/cryptogamic-herbarium.html
Herbarium specimens of Bathelium mastoideum (2) and Bogoriella megaspora (1) used for metagenome sequencing	Herbarium ABL	http://sweetgum.nybg.org/science/ih/ herbarium-details/?irn=123895
Herbarium specimen of Candelina mexicana used for metagenome sequencing	Herbarium CUVC	http://sweetgum.nybg.org/science/ ih/herbarium-details/?irn=126294
All remaining 29 herbarium specimens used for generating new metagenomes	Herbarium UPS	http://www.evolutionsmuseet.uu.se/ databaser/databaseseng.html
Fungal culture of Cirrosporium novae-zelandiae used for generating genome	Westerdijk Fungal Biodiversity Institute (CBS)	https://wi.knaw.nl/page/fungal_table
Critical commercial assays
QIAamp DNA Investigator Kit	QIAGEN	Cat#56504
DNeasy Plant Mini Kit	QIAGEN	Cat#69104
Illumina DNA Prep, (M) Tagmentation	Illumina	Cat#20018704
Nextera DNA CD Indexes	Illumina	Cat#20018707
TruSeq DNA PCR-Free Low Throughput Library Prep Kit	Illumina	Cat#20015962
Deposited data
Raw Sequencing Reads	This paper	NCBI: SRR19097865–SRR19097892 (https://www.ncbi.nlm.nih.gov)
Assembled and annotated genomes	This paper	NCBI: JAPETH000000000– JAPEUK000000000 (https://www.ncbi.nlm.nih.gov)
Software and algorithms
FastQC v0.11.9	Andrews56	https://www.bioinformatics.babraham.ac.uk/ projects/fastqc/
Trimmomatic v0.39	Bolger et al.57	https://github.com/usadellab/Trimmomatic
SPAdes v3.13.1, v3.14.1, v3.15.1	Nurk et al.58	https://github.com/ablab/spades
Bowtie2 v2.3.5.1 CONCOCT v1.1.0	Langmead and Salzberg59 Alneberg et al.60	http://bowtie-bio.sourceforge.net/bowtie2/ index.shtml https://github.com/BinPro/CONCOCT
BlobTools EukCC v0.1.5.1	Laetsch and Blaxter61 Saary et al.62	https://github.com/DRL/blobtools https://github.com/Finn-Lab/EukCC
BUSCO v2.0.0, v3.0.2, v5.2.1 MetaWrap(Quant_bins Module) v1.3.2	Simão et al.,63 Waterhouse et al.,64 Manni et al.65 Uritskiy et al.66	http://busco.ezlab.org https://github.com/bxlab/metaWRAP
Salmon v0.13.1 (within MetaWrap)	Patro et al.67	https://github.com/COMBINE-lab/salmon
Samtools v1.9	Li et al.68	http://www.htslib.org
BLAST+ v2.2.31, v2.6.0, v2.9.0, v2.11+ IQTree v2.0.7, v2.1.3	Camacho et al.69 Minh et al.70	https://ftp.ncbi.nlm.nih.gov/blast/ executables/blast+/ http://www.iqtree.org
Phylociraptor v0.9.3	Phylociraptor	https://github.com/reslp/phylociraptor
MAFFT v7.464	Katoh and Standley71	https://mafft.cbrc.jp/alignment/software/
trimAL v1.4.1	Capella-Gutierrez et al.72	http://trimal.cgenomics.org
ASTRALv5.7.1	Zhang et al.73	https://github.com/smirarab/ASTRAL