ArticlePloS one2011
Universally distributed single-copy genes indicate a constant rate of horizontal transfer.
Article in PloS one, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 59 papers.
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59 citing papers in PubMed.
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- Generation of accurate, expandable phylogenomic trees with uDance.Nature biotechnology · 2024Article
- VBCG: 20 validated bacterial core genes for phylogenomic analysis with high fidelity and resolution.Microbiome · 2023Article
- Horizontal Gene Transfer and Drug Resistance InvolvingAntibiotics (Basel, Switzerland) · 2023Article
- OrthoVenn3: an integrated platform for exploring and visualizing orthologous data across genomes.Nucleic acids research · 2023Article
- Incompatibility and Interchangeability in Molecular Evolution.Genome biology and evolution · 2023Review
- A revisit to universal single-copy genes in bacterial genomes.Scientific reports · 2022Article
- Comprehensive Phylogenomics of Methylobacterium Reveals Four Evolutionary Distinct Groups and Underappreciated Phyllosphere Diversity.Genome biology and evolution · 2022Article
- An expanded reference map of the human gut microbiome reveals hundreds of previously unknown species.Nature communications · 2022Article
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- Growth promotion and antibiotic induced metabolic shifts in the chicken gut microbiome.Communications biology · 2022Article
- An estimate of the deepest branches of the tree of life from ancient vertically evolving genes.eLife · 2022Article
- Novel nitrite reductase domain structure suggests a chimeric denitrification repertoire in the phylum Chloroflexi.MicrobiologyOpen · 2022Article
- Assembling a Reference Phylogenomic Tree of Bacteria and Archaea by Summarizing Many Gene Phylogenies.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Phylogenetic Signal, Congruence, and Uncertainty across Bacteria and Archaea.Molecular biology and evolution · 2021Article
- Phylogenetic systematics ofMicrobial genomics · 2021Article
- Evidence for Selection in the Abundant Accessory Gene Content of a Prokaryote Pangenome.Molecular biology and evolution · 2021Article
- Reductive evolution and unique predatory mode in the CPR bacterium Vampirococcus lugosii.Nature communications · 2021Article
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5 authors.
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Abstract
Single copy genes, universally distributed across the three domains of life and encoding mostly ancient parts of the translation machinery, are thought to be only rarely subjected to horizontal gene transfer (HGT). Indeed it has been proposed to have occurred in only a few genes and implies a rare, probably not advantageous event in which an ortholog displaces the original gene and has to function in a foreign context (orthologous gene displacement, OGD). Here, we have utilised an automatic method to identify HGT based on a conservative statistical approach capable of robustly assigning both donors and acceptors. Applied to 40 universally single copy genes we found that as many as 68 HGTs (implying OGDs) have occurred in these genes with a rate of 1.7 per family since the last universal common ancestor (LUCA). We examined a number of factors that have been claimed to be fundamental to HGT in general and tested their validity in the subset of universally distributed single copy genes. We found that differing functional constraints impact rates of OGD and the more evolutionarily distant the donor and acceptor, the less likely an OGD is to occur. Furthermore, species with larger genomes are more likely to be subjected to OGD. Most importantly, regardless of the trends above, the number of OGDs increases linearly with time, indicating a neutral, constant rate. This suggests that levels of HGT above this rate may be indicative of positively selected transfers that may allow niche adaptation or bestow other benefits to the recipient organism.
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