ArticleBMC evolutionary biology2009
Horizontal Gene Transfers in prokaryotes show differential preferences for metabolic and translational genes.
Article in BMC evolutionary biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Horizontal transfer of post-translational modifiers brings evolutionary opportunity and challenges to a conserved translation factor.BMC biology · 2026Article
- Article
- Genetic exchange shapes ultra-small Patescibacteria metabolic capacities in the terrestrial subsurface.mSystems · 2025Article
- Orphan genes are not a distinct biological entity.BioEssays : news and reviews in molecular, cellular and developmental biology · 2025Review
- Horizontal Gene Transfer of a key Translation Factor and its Role in Polyproline Proteome Evolution.Molecular biology and evolution · 2024Article
- The Theory of Gene Family Histories.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Insights into early evolutionary adaptations of theFrontiers in microbiology · 2023Article
- Encapsulins.Annual review of biochemistry · 2022Review
- Large-scale computational discovery and analysis of virus-derived microbial nanocompartments.Nature communications · 2021Article
- Indirect identification of horizontal gene transfer.Journal of mathematical biology · 2021Article
- Article
- Evolutionary and Comparative Analysis of Bacterial Nonhomologous End Joining Repair.Genome biology and evolution · 2020Article
- Current and Promising Approaches to Identify Horizontal Gene Transfer Events in Metagenomes.Genome biology and evolution · 2019Review
- Article
- Review
- Article
- One step beyond a ribosome: The ancient anaerobic core.Biochimica et biophysica acta · 2016Review
- Bacterial gene import and mesophilic adaptation in archaea.Nature reviews. Microbiology · 2015Review
- Pangenome evidence for extensive interdomain horizontal transfer affecting lineage core and shell genes in uncultured planktonic thaumarchaeota and euryarchaeota.Genome biology and evolution · 2014Article
- Being Aquifex aeolicus: Untangling a hyperthermophile's checkered past.Genome biology and evolution · 2013Article
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Authors and funding
2 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundHorizontal gene transfer (HGT) is an important process, which contributes in bacterial pathogenesis and drug resistance. A number of methods have been proposed for detection of horizontal gene transfer. One successful approach to the detection of HGT events is due to Novichkov et al. (J. Bacteriology 186, 6575-85), who rely on comparing phylogenetic distances within a gene family with genomic distances of the source organisms. Building on their approach, we introduce outlier detection in the correlation between those two sets of distances. This approach is designed to detect horizontal transfers of core set of genes present in many bacteria. The principle behind method allows detection of xenologous gene displacements as well as acquisition of novel genes.
resultsSimulations indicated that our method performs better than Novichkov et al's original approach. The approach very efficiently identified HGT between distantly related bacteria and also a limited number of gene transfers between closely related bacteria. In combination with sequence similarity and likelihood tests, it yields a measure robust enough to derive a set of 171 genes deemed likely to have been horizontally transferred. Further analysis of these 171 established horizontal transfer events gave interesting insights in the direction of transfer.
conclusionThe majority of transfers between archaea and bacteria have occurred in the direction from bacteria to archaea rather than the other way round. Genes transferred between the archaea and bacteria are mostly metabolic genes. On the other hand, genes transferred within the bacterial phyla are mainly involved in translation.
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