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Related Concept Videos

Horizontal Gene Transfer01:27

Horizontal Gene Transfer

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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:...
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Types of Genetic Transfer Between Organisms02:18

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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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Conjugation01:19

Conjugation

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Conjugation is a form of horizontal gene transfer that primarily occurs in bacteria and some archaea, promoting genetic diversity and adaptation. Bacteria can acquire resistance genes through conjugative plasmids, allowing them to survive antibiotic treatments that would otherwise be lethal. This process involves direct contact between cells through specialized structures such as the sex pilus and is mediated by conjugative plasmids, including the F (fertility) factor.Conjugation requires...
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Coordination of Gene Expression Processes in Bacteria01:29

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The DNA replication, transcription, and translation processes are intricately coupled in bacteria, allowing efficient gene expression and rapid protein synthesis. While this physical and functional coordination is advantageous, it introduces challenges that bacteria overcome through specific regulatory mechanisms.Coupling of Replication, Transcription, and TranslationThe coupling of replication, transcription, and translation is a hallmark of bacterial gene expression. As the replisome unwinds...
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Transduction01:16

Transduction

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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...
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Detection of Horizontal Gene Transfer Mediated by Natural Conjugative Plasmids in E. coli
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GeneMates: an R package for detecting horizontal gene co-transfer between bacteria using gene-gene associations

Yu Wan1, Ryan R Wick2,3, Justin Zobel4

  • 1Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, 3010, Victoria, Australia. wanyuac@126.com.

BMC Genomics
|September 25, 2020
PubMed
Summary

We developed GeneMates, a network approach to detect horizontal gene co-transfer (HGcoT) within bacterial species using whole-genome sequencing data. This method accurately identifies co-transferred genes, overcoming limitations of traditional association tests.

Keywords:
Acquired genesAssociation analysisHorizontal gene transferLinear mixed modelsMobile genetic elementsNetwork approachPhysical linkagePopulation structurePrincipal componentsR package

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Area of Science:

  • Microbiology
  • Genomics
  • Bioinformatics

Background:

  • Horizontal gene transfer (HGT) drives bacterial evolution and the spread of important genes.
  • Mobile genetic elements (MGEs) mediate HGT, leading to horizontal gene co-transfer (HGcoT).
  • Previous methods for studying HGcoT using whole-genome sequencing (WGS) data were confounded by bacterial population structure.

Purpose of the Study:

  • To develop a robust network approach for detecting intraspecies HGcoT from WGS data.
  • To create an R package, GeneMates, to implement this novel network analysis.

Main Methods:

  • Developed a network approach analyzing allelic presence-absence matrices and core-genome SNPs.
  • Implemented association tests using linear mixed models to control for population structure.
  • Incorporated physical distance scoring of alleles within genome assemblies for HGcoT evidence.

Main Results:

  • GeneMates successfully identifies clusters of co-transferred alleles within bacterial populations.
  • The network approach distinguishes HGcoT from clonal reproduction and accounts for population structure.
  • Validation studies in *Escherichia coli* and *Salmonella Typhimurium* demonstrated the method's effectiveness.

Conclusions:

  • GeneMates provides an effective and reliable method for detecting intraspecies HGcoT.
  • This approach enhances our understanding of gene dissemination in bacterial populations.