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Related Concept Videos

Horizontal Gene Transfer01:27

Horizontal Gene Transfer

65
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:...
65
Transduction01:16

Transduction

68
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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Types of Genetic Transfer Between Organisms02:18

Types of Genetic Transfer Between Organisms

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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

57
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...
57
Modern Molecular Taxonomy01:29

Modern Molecular Taxonomy

77
Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
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RNA-seq03:21

RNA-seq

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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
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Related Experiment Video

Updated: Aug 18, 2025

Transposon-insertion Sequencing as a Tool to Elucidate Bacterial Colonization Factors in a Burkholderia gladioli Symbiont of Lagria villosa Beetles
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hgtseq: A Standard Pipeline to Study Horizontal Gene Transfer.

Simone Carpanzano1, Mariangela Santorsola1, Nf-Core Community1

  • 1Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy.

International Journal of Molecular Sciences
|December 11, 2022
PubMed
Summary

Horizontal gene transfer (HGT) is crucial in evolution but less understood in humans. We present nf-core/hgtseq, a tool to systematically investigate HGT from sequencing data, aiding future research.

Keywords:
bioinformatic pipelinesexomehorizontal gene transfermicrobiomesequencing

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Methodology for the Study of Horizontal Gene Transfer in Staphylococcus aureus
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Area of Science:

  • Genomics
  • Evolutionary Biology
  • Bioinformatics

Background:

  • Horizontal gene transfer (HGT) is a significant evolutionary mechanism in prokaryotes, insects, and plants.
  • The extent and mechanisms of HGT in humans remain largely unexplored, despite evidence of microbial integrations in human studies.
  • Existing tools for HGT investigation often lack high levels of automation.

Purpose of the Study:

  • To introduce nf-core/hgtseq, a novel, automated bioinformatics pipeline for analyzing HGT from sequencing data.
  • To provide a standardized and scalable tool for investigating HGT across different organisms, including humans.
  • To facilitate a systematic approach to understanding the role and extent of HGT.

Main Methods:

  • Development of a Nextflow-based pipeline, nf-core/hgtseq, adhering to nf-core standards.
  • Application of the pipeline to analyze six exome datasets from five mammalian species.
  • Ensuring the pipeline's portability and scalability across diverse computing environments.

Main Results:

  • Demonstrated the performance of nf-core/hgtseq on mammalian exome data.
  • Confirmed the pipeline's ability to run seamlessly in various computational settings.
  • Showcased compatibility with existing exome and whole-genome sequencing data.

Conclusions:

  • nf-core/hgtseq offers a standardized, automated, and scalable solution for HGT analysis.
  • The tool enables researchers to readily investigate HGT in their sequencing data, expanding research scope.
  • Facilitates systematic investigation into the open questions surrounding HGT mechanisms, extent, and role in evolution.