ArticlePLoS computational biology2015
Detecting Horizontal Gene Transfer between Closely Related Taxa.
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 37 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
37 citing papers in PubMed.
- A machine learning framework for interpreting phylogenetic tree patterns in interkingdom horizontal gene transfer.Frontiers in bioinformatics · 2026Article
- Phylogenetic and genomic insights into magnetosome biomineralization in magnetotacticApplied and environmental microbiology · 2025Article
- Genomic data representations for horizontal gene transfer detection.NAR genomics and bioinformatics · 2025Article
- Mechanisms, detection, and impact of horizontal gene transfer in plant functional evolution.The Plant cell · 2025Review
- Strain tracking in complex microbiomes using synteny analysis reveals per-species modes of evolution.Nature biotechnology · 2025Article
- Multiple Horizontal Transfers of Immune Genes Between Distantly Related Teleost Fishes.Molecular biology and evolution · 2025Article
- Paradox of the Sub-Plankton: Plausible Mechanisms and Open Problems Underlying Strain-Level Diversity in Microbial Communities.Environmental microbiology · 2025Review
- Current state and future prospects of Horizontal Gene Transfer detection.NAR genomics and bioinformatics · 2025Review
- The priority of yeast to select among various DNA options to repair genome breaks by homologous recombination.Molecular biology reports · 2024Article
- Detecting horizontal gene transfer among microbiota: an innovative pipeline for identifying co-shared genes within the mobilome through advanced comparative analysis.Microbiology spectrum · 2024Article
- Origins and Evolution of NovelbioRxiv : the preprint server for biology · 2023Article
- HGTree v2.0: a comprehensive database update for horizontal gene transfer (HGT) events detected by the tree-reconciliation method.Nucleic acids research · 2023Article
- A complete theoretical framework for inferring horizontal gene transfers using partial order sets.PloS one · 2023Article
- hgtseq: A Standard Pipeline to Study Horizontal Gene Transfer.International journal of molecular sciences · 2022Article
- The Role of the Environment in Horizontal Gene Transfer.Molecular biology and evolution · 2022Article
- Ghost lineages can invalidate or even reverse findings regarding gene flow.PLoS biology · 2022Article
- Current Methods for Recombination Detection in Bacteria.International journal of molecular sciences · 2022Review
- Old genes in new places: A taxon-rich analysis of interdomain lateral gene transfer events.PLoS genetics · 2022Article
- Relation between two evolutionary clocks reveal new insights in bacterial evolution.Access microbiology · 2022Article
- Genomes of NovelApplied and environmental microbiology · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Horizontal gene transfer (HGT), the transfer of genetic material between organisms, is crucial for genetic innovation and the evolution of genome architecture. Existing HGT detection algorithms rely on a strong phylogenetic signal distinguishing the transferred sequence from ancestral (vertically derived) genes in its recipient genome. Detecting HGT between closely related species or strains is challenging, as the phylogenetic signal is usually weak and the nucleotide composition is normally nearly identical. Nevertheless, there is a great importance in detecting HGT between congeneric species or strains, especially in clinical microbiology, where understanding the emergence of new virulent and drug-resistant strains is crucial, and often time-sensitive. We developed a novel, self-contained technique named Near HGT, based on the synteny index, to measure the divergence of a gene from its native genomic environment and used it to identify candidate HGT events between closely related strains. The method confirms candidate transferred genes based on the constant relative mutability (CRM). Using CRM, the algorithm assigns a confidence score based on "unusual" sequence divergence. A gene exhibiting exceptional deviations according to both synteny and mutability criteria, is considered a validated HGT product. We first employed the technique to a set of three E. coli strains and detected several highly probable horizontally acquired genes. We then compared the method to existing HGT detection tools using a larger strain data set. When combined with additional approaches our new algorithm provides richer picture and brings us closer to the goal of detecting all newly acquired genes in a particular strain.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.