ArticlePLoS computational biology2015
Inferring horizontal gene transfer.
Article in PLoS computational biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 150 papers.
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150 citing papers in PubMed.
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- Widespread genomic islands are hotspots of genome variations and mosaicism in giant viruses.Nature communications · 2026Article
- Comparative transcriptomics and scarless genome editing uncover a periplasmicApplied and environmental microbiology · 2026Article
- Horizontal gene transfer in Saccharomyces cerevisiae and other Saccharomycotina yeasts: a review.World journal of microbiology & biotechnology · 2026Review
- A compendium of horizontal gene transfers in Metazoa.Scientific data · 2026Article
- Reconstructing the Network of Horizontal Gene Exchange in Bacteria to Differentiate Direct and Indirect Transfers.Genome biology and evolution · 2026Article
- Lifestyle-associated variation in type IV secretion systems between phytopathogenic and environmentalMicrobial genomics · 2026Article
- TreeProfiler: large-scale metadata profiling along gene and species trees.Molecular biology and evolution · 2026Article
- Adaptation of Fe-S Cluster Assembly to Rising OResearch square · 2026Article
- A machine learning framework for interpreting phylogenetic tree patterns in interkingdom horizontal gene transfer.Frontiers in bioinformatics · 2026Article
- A Gifsy prophage-encoded protein confers broad phage resistance inApplied and environmental microbiology · 2025Article
- Reconstructing Evolutionary Histories with Hierarchical Orthologous Groups.Journal of molecular evolution · 2025Review
- Core genome expansion inIranian journal of microbiology · 2025Article
- Dating the Bacterial Tree of Life Based on Ancient Symbiosis.Systematic biology · 2025Article
- Leveraging FracMinHash Containment for GenomicbioRxiv : the preprint server for biology · 2025Article
- The eukaryotic horizontal gene transfer dataset a compendium.bioRxiv : the preprint server for biology · 2025Article
- Closed genome sequence of anMicrobiology resource announcements · 2025Article
- Inference of Cytochrome P450 Evolutionary History Using Structural and Physicochemical Metrics.Genome biology and evolution · 2025Article
90 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Horizontal or Lateral Gene Transfer (HGT or LGT) is the transmission of portions of genomic DNA between organisms through a process decoupled from vertical inheritance. In the presence of HGT events, different fragments of the genome are the result of different evolutionary histories. This can therefore complicate the investigations of evolutionary relatedness of lineages and species. Also, as HGT can bring into genomes radically different genotypes from distant lineages, or even new genes bearing new functions, it is a major source of phenotypic innovation and a mechanism of niche adaptation. For example, of particular relevance to human health is the lateral transfer of antibiotic resistance and pathogenicity determinants, leading to the emergence of pathogenic lineages. Computational identification of HGT events relies upon the investigation of sequence composition or evolutionary history of genes. Sequence composition-based ("parametric") methods search for deviations from the genomic average, whereas evolutionary history-based ("phylogenetic") approaches identify genes whose evolutionary history significantly differs from that of the host species. The evaluation and benchmarking of HGT inference methods typically rely upon simulated genomes, for which the true history is known. On real data, different methods tend to infer different HGT events, and as a result it can be difficult to ascertain all but simple and clear-cut HGT events.
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