Divergent genomic trajectories predate the origin of animals and fungi

22 pages, 4 figures, supplementary information https://doi.org/10.1038/s41586-022-05110-4.-- Data availability: The raw sequence data and assembled genomes generated in this study have been deposited in the European Nucleotide Archive (ENA) at EMBL-EBI under accession number PRJEB52884 (https://www.ebi.ac.uk/ena/browser/view/PRJEB52884). The genome assemblies are also available in figshare (https://doi.org/10.6084/m9.figshare.19895962.v1). Protein sequences of the species used in this study were downloaded from the GenBank public databases (https://www.ncbi.nlm.nih.gov/protein/), Uniprot (https://www.uniprot.org/), JGI genome database (https://genome.jgi.doe.gov/portal/) and Ensembl genomes (https://www.ensembl.org). The following specific databases were also used in this study: Pfam A v29 (https://pfam.xfam.org/), EggNOG emapperdb-4.5.1 (http://eggnog5.embl.de) and UniProt reference proteomes release 2016_02 (https://www.uniprot.org/). The supporting data files of this study are available in the following repository: https://doi.org/10.6084/m9.figshare.13140191.v1.-- Code availability: The most relevant custom code developed for this study (the MAPBOS pipeline and the machine learning classifiers) is available at https://doi.org/10.5281/zenodo.6586559