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Updated: Jul 4, 2026
06:56
Detection of Horizontal Gene Transfer Mediated by Natural Conjugative Plasmids in E. coli
Published on: March 24, 2023
Unsupervised learning in detection of gene transfer.
L Hamel1, N Nahar, M S Poptsova
1Department of Computer Science and Statistics, University of Rhode Island, Kingston, RI 02881, USA. hamel@cs.uri.edu
Journal of Biomedicine & Biotechnology
|May 30, 2008
Summary
Evolutionary trees for organisms are complex. Analyzing gene histories reveals a consensus evolutionary tree, with conflicting gene trees potentially indicating horizontal gene transfer events.
Area of Science:
- Genomics
- Evolutionary Biology
- Bioinformatics
Background:
- The traditional view of organismal evolution relies on a single evolutionary tree.
- Genomic data reveals conflicting evolutionary histories among individual genes, particularly in microbes.
- This challenges the concept of a singular organismal evolutionary tree.
Purpose of the Study:
- To propose a novel approach for analyzing genomic data to understand evolutionary relationships.
- To reconcile conflicting gene tree topologies within a genome.
- To identify significant evolutionary events like horizontal gene transfer.
Main Methods:
- Utilizing bipartition spectral analysis for genomic data.
- Applying unsupervised learning techniques to identify patterns in gene histories.
- Comparing individual gene trees against a derived evolutionary consensus tree.
Main Results:
- Developed a method to construct an evolutionary consensus tree from genomic data.
- Identified genes with topologies conflicting with the consensus tree.
- Observed that conflicting gene trees correlate with potential horizontal gene transfer events.
Conclusions:
- The notion of an evolutionary consensus tree provides a more accurate model for organismal evolution, especially for microbes.
- Analysis of gene tree conflicts can reveal significant evolutionary events, such as horizontal gene transfer.
- This approach offers new insights into the complex network of gene histories within genomes.
Related Concept Videos
02:18Types of Genetic Transfer Between Organisms
Genetic transfer occurs when genetic information is passed from one organism to another. It occurs via two mechanisms: vertical gene transfer and horizontal gene transfer. Vertical gene transfer occurs when genetic information is transferred from one generation to the next, which happens much more frequently than horizontal gene transfer. Both sexual and asexual reproduction are forms of vertical gene transfer, where one or more organisms pass some or all of their genome onto their progeny.
02:18Types of Genetic Transfer Between Organisms
Genetic transfer occurs when genetic information is passed from one organism to another. It occurs via two mechanisms: vertical gene transfer and horizontal gene transfer. Vertical gene transfer occurs when genetic information is transferred from one generation to the next, which happens much more frequently than horizontal gene transfer. Both sexual and asexual reproduction are forms of vertical gene transfer, where one or more organisms pass some or all of their genome onto their progeny.
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Among the three main modes of HGT—transformation, conjugation, and transduction—transduction is unique in that it is mediated by bacteriophages, or bacterial viruses.Transduction occurs in two ways. Generalized transduction occurs during the lytic cycle of a bacteriophage infection. In this process, bacteriophages infect bacterial cells, replicate within them, and ultimately cause cell lysis, releasing newly assembled virions. Occasionally, random fragments of the bacterial genome are...
01:27Horizontal Gene Transfer
Horizontal gene transfer (HGT) is a process where genetic material moves between organisms within the same generation, unlike vertical gene transfer, which occurs from parent to offspring. HGT plays a crucial role in microbial evolution, adaptation, and survival, particularly in shared environments like the human gut.Mobile genetic elements such as plasmids, prophages, integrons, insertion sequences, and transposons facilitate this process. HGT occurs through three primary mechanisms:...
03:21Genome Size and the Evolution of New Genes
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02:11Reporter Genes
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Commonly used reporter...
Commonly used reporter...