ArticleScientific reports2022
A revisit to universal single-copy genes in bacterial genomes.
Article in Scientific reports, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Augmenting microbial phylogenomic signal with tailored marker gene sets.Nature communications · 2025Article
- Portal vein-enriched metabolites as intermediate regulators of the gut microbiome in insulin resistance.Cell metabolism · 2025Article
- Species-resolved profiling of antibiotic resistance genes in complex metagenomes through long-read overlapping with Argo.Nature communications · 2025Article
- Net rate of lateral gene transfer in marine prokaryoplankton.The ISME journal · 2025Article
- qPCR-based quantification reveals high plant host-specificity of endophytic colonization levels in leaves.American journal of botany · 2025Article
- GCompip: a pipeline for estimating the gene abundance in microbial communities.Bioinformatics advances · 2025Article
- Database size positively correlates with the loss of species-level taxonomic resolution for the 16S rRNA and other prokaryotic marker genes.PLoS computational biology · 2024Article
- Iron Chelation in Soil: Scalable Biotechnology for Accelerating Carbon Dioxide Removal by Enhanced Rock Weathering.Environmental science & technology · 2024Article
- Protein-Coding Gene Families in Prokaryote Genome Comparisons.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Combining 16S Sequencing and qPCR Quantification RevealsBiomolecules · 2023Article
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Universal single-copy genes (USCGs) are widely used for species classification and taxonomic profiling. Despite many studies on USCGs, our understanding of USCGs in bacterial genomes might be out of date, especially how different the USCGs are in different studies, how well a set of USCGs can distinguish two bacterial species, whether USCGs can separate different strains of a bacterial species, to name a few. To fill the void, we studied USCGs in the most updated complete bacterial genomes. We showed that different USCG sets are quite different while coming from highly similar functional categories. We also found that although USCGs occur once in almost all bacterial genomes, each USCG does occur multiple times in certain genomes. We demonstrated that USCGs are reliable markers to distinguish different species while they cannot distinguish different strains of most bacterial species. Our study sheds new light on the usage and limitations of USCGs, which will facilitate their applications in evolutionary, phylogenomic, and metagenomic studies.
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