Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Viral Recombination

Viral Recombination

Cells are sometimes infected by more than one virus at once. When two viruses disassemble to expose their genomes for replication in the same cell, similar regions of their genomes can pair together and exchange sequences in a process called recombination. Alternatively, viruses with segmented genomes can swap segments in a process called reassortment.

Conservative Site-specific Recombination and Phase Variation

Conservative Site-specific Recombination and Phase Variation

Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
The recognition sites for Cre recombinase called LoxP...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

Narrowed host ranges do not constrain future host range expansion in RNA phage Φ6.

Journal of virology·2026

Same author

Outbreak of H9N2 avian influenza viruses in lesser rhea in Peru, June-July 2025.

bioRxiv : the preprint server for biology·2026

Same author

Emergence of D1.1 reassortant H5N1 avian influenza viruses in North America.

bioRxiv : the preprint server for biology·2026

Same author

The emergence and molecular evolution of H5N1 influenza viruses in United States dairy cattle.

bioRxiv : the preprint server for biology·2026

Same author

<i>Begomovirus</i> species demarcation based on genome-sequence identity yields non-monophyletic species: a case study of sweet potato-infecting begomoviruses.

Virus evolution·2026

Same author

Can H5N1 avian influenza in dairy cattle be contained in the US?

Cell·2026

Same journal

Mapping the 3D Chromosome Organization of a Biosynthetic Gene Cluster by Capture Hi-C (CHi-C).

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

Mapping the 3D Chromosome Organization of Streptomyces by Hi-C.

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

CUT&Tag Epigenomic Profiling of Biosynthetic Gene Clusters in Arabidopsis thaliana.

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

Rhizobium rhizogenes-Mediated Hairy Root Transformation Protocol for Lotus japonicus and Other Legumes.

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

Characterization of Bioactive Saponins from Sea Cucumbers.

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

Methods for Functional Validation of Terpenoid Metabolic Clusters in Nicotiana benthamiana and Aspergillus oryzae.

Methods in molecular biology (Clifton, N.J.)·2026

See all related articles

Search research articles

Related Experiment Video

Updated: May 23, 2025

Combining Analysis of DNA in a Crude Virion Extraction with the Analysis of RNA from Infected Leaves to Discover New Virus Genomes

Combining Analysis of DNA in a Crude Virion Extraction with the Analysis of RNA from Infected Leaves to Discover New Virus Genomes

Published on: July 27, 2018

Recombination Analysis of Geminiviruses Using Recombination Detection Program (RDP).

Alvin Crespo-Bellido¹, Darren Patrick Martin², Siobain Duffy³

¹Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA.

Methods in Molecular Biology (Clifton, N.J.)

|March 11, 2025

Summary

This summary is machine-generated.

Researchers frequently study recombination in geminiviruses. This study details using RDP4 and RDP5 software to analyze geminiviral DNA sequences, identify recombination, and create datasets for further molecular evolution studies.

Keywords:

Evolution Horizontal gene transfer Multiple sequence alignment Phylogenetics RDP5 Recombination Sub-alignment

More Related Videos

Bidirectional Retroviral Integration Site PCR Methodology and Quantitative Data Analysis Workflow

Bidirectional Retroviral Integration Site PCR Methodology and Quantitative Data Analysis Workflow

Published on: June 14, 2017

Amplification, Next-generation Sequencing, and Genomic DNA Mapping of Retroviral Integration Sites

Amplification, Next-generation Sequencing, and Genomic DNA Mapping of Retroviral Integration Sites

Published on: March 22, 2016

Related Experiment Videos

Last Updated: May 23, 2025

Combining Analysis of DNA in a Crude Virion Extraction with the Analysis of RNA from Infected Leaves to Discover New Virus Genomes

Combining Analysis of DNA in a Crude Virion Extraction with the Analysis of RNA from Infected Leaves to Discover New Virus Genomes

Published on: July 27, 2018

Bidirectional Retroviral Integration Site PCR Methodology and Quantitative Data Analysis Workflow

Bidirectional Retroviral Integration Site PCR Methodology and Quantitative Data Analysis Workflow

Published on: June 14, 2017

Amplification, Next-generation Sequencing, and Genomic DNA Mapping of Retroviral Integration Sites

Amplification, Next-generation Sequencing, and Genomic DNA Mapping of Retroviral Integration Sites

Published on: March 22, 2016

Area of Science:

Virology
Molecular Evolution
Bioinformatics

Background:

Geminiviruses are known for frequent recombination events.
Understanding geminiviral evolution requires characterizing genome recombination.
The Recombination Detection Program (RDP) is a widely used tool for this purpose.

Purpose of the Study:

To describe the application of RDP4 and RDP5 for analyzing geminiviral nucleotide sequences.
To guide researchers in preparing datasets and alignments for recombination analysis.
To demonstrate RDP's utility in identifying recombination and generating recombination-free datasets.

Main Methods:

Utilizing RDP4 and RDP5 software for sequence analysis.
Dataset preparation for geminiviral nucleotide sequences.
Performing multiple sequence alignment.
Applying RDP algorithms to detect and characterize recombination.

Main Results:

Successful application of RDP4 and RDP5 to geminiviral sequences.
Characterization of recombination events within geminiviral genomes.
Generation of statistically recombination-free datasets for downstream analyses.

Conclusions:

RDP4 and RDP5 are effective tools for studying geminiviral recombination.
The described methods facilitate robust analysis of viral evolution.
This approach aids in producing reliable datasets for molecular evolution research.