biostudies-literatureUnknown23(1)Alam MNUBud Antle Endowed Chair of Excellence in Agriculture &amp; Life Sciences awarded to Rod A. Wing at the University of Arizona<h4>Background</h4>Universal single-copy orthologs are the most conserved components of genomes. Although they are routinely used for studying evolutionary histories and assessing new assemblies, current methods do not incorporate information from available genomic data.<h4>Results</h4>Here, we first determine the influence of evolutionary history on universal gene content and find that across 11,098 genomes of plants, fungi, and animals comprising 2606 taxonomic groups, 215 groups significantly vary from their respective lineages in terms of BUSCO (Benchmarking Universal Single Copy Orthologs) completeness. Additionally, 169 groups display an elevated complement of duplicated orthologs, likely from ancestral whole genome duplication events. Secondly, we investigate the extent of taxonomicBMC biology224https://www.ebi.ac.uk/biostudies/studies/S-EPMC12302877biostudies-literatureUniversal orthologs infer deep phylogenies and improve genome quality assessments.PMC12302877Roman-Palacios CAlam MNUCopetti DWing RAfalseUniversal orthologs infer deep phylogenies and improve genome quality assessments.<h4>Background</h4>Universal single-copy orthologs are the most conserved components of genomes. Although they are routinely used for studying evolutionary histories and assessing new assemblies, current methods do not incorporate information from available genomic data.<h4>Results</h4>Here, we first determine the influence of evolutionary history on universal gene content and find that across 11,098 genomes of plants, fungi, and animals comprising 2606 taxonomic groups, 215 groups significantly vary from their respective lineages in terms of BUSCO (Benchmarking Universal Single Copy Orthologs) completeness. Additionally, 169 groups display an elevated complement of duplicated orthologs, likely from ancestral whole genome duplication events. Secondly, we investigate the extent of taxonomic2025-01-01T00:00:00Z2025 Jul2026-07-15T05:58:52.087Z2025-08-18T09:52:44.815ZS-EPMC123028774071706310.1186/s12915-025-02328-2