Reagent or Resource	Source	Identifier
Deposited data
DNA and RNA sequences	This Paper	https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA666913
VEuPathDB	VeuPathDB	https://veupathdb.org/veupathdb/app
Aniseed	aniseed	https://www.aniseed.cnrs.fr/aniseed/species/
Busco v3	Swiss Institute of Bioinformatics	https://busco.ezlab.org/
Interproscan v71.0	InterPro	https://www.ebi.ac.uk/interpro/about/interproscan/
KEGG	Kanehisa Laboratories	https://www.kegg.jp/
Software and algorithms
Trimmomatic v0.3	USADELL Lab	http://www.usadellab.org/cms/?page=trimmomatic
SPAdes v3.13.	Saint Petersburg State University	https://github.com/ablab/spades
PBSuite v15.8.2	Pacific Biosciences	https://sourceforge.net/projects/pb-jelly/
Canu v1.6	Maryland Bioinformatics Labs	https://github.com/marbl/canu/releases/tag/v2.2
ABySS v2.02	BC Cancer Canada’s Michael Smith Genome Sciences Centre	https://github.com/bcgsc/abyss
Bowtie2 v1.2.2	Johns Hopkins University	http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
Bedtools	University of Utah	https://bedtools.readthedocs.io/en/latest/index.html
VizBin	university du luxembourg	https://claczny.github.io/VizBin/
CAT	Universiteit Utrecht	https://github.com/dutilh/CAT
Trinity/Trinotate pipeline v2.4.0	The Broad Institute	https://github.com/trinityrnaseq/trinityrnaseq
BLASTp	National Center for Biotechnology Information	ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/
Transdecoder	The Broad Institute	https://github.com/TransDecoder/TransDecoder
BBmap	Brian Bushnell	https://sourceforge.net/projects/bbmap/
CDhit v4.6.8	UCSD	https://sourceforge.net/projects/cdhit/
Prokka	The University of Melbourne	https://github.com/tseemann/prokka
Maker	University of Utah	http://www.yandell-lab.org/software/maker.html
R and bash code	This paper	https://github.com/cpaight/Nephromyces
Critical commercial assays
MiSeq Reagent Kit v3	Illumina	Product Number MS-102–3003
HiSeq 2500 2×250 HiSeq SBS v4	Illumina	Product Number FC-401–4003
SMRT cells	Pacific Biosciences	Product Number 102-281-700
Zymo Quick-RNA kit	Zymo	Catalogue number R1054
Illumina TruSeq RNA kit	Illumina	Product Number RS-122–2001
Prolong Gold with DAPI	ThermoFisher	Product Number P-36931
Experimental models: Organisms/strains
M. manhattensis	This paper	Live collection, Greenwich Bay, RI (41.653N, −71.452W)
M. occidentalis	This paper	Live collection by Gulf Specimens Marine Laboratories, Inc. from Alligator Harbor, FL (29.899N, −84.381W)
Isochrysis galbana	National Center for Marine Algae and Microbiota	CCMP1323
Chaetoceras sp.	National Center for Marine Algae and Microbiota	CCMP209