Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Overview of Transposition and Recombination02:13

Overview of Transposition and Recombination

Transposons make up a significant part of genomes of various organisms. Therefore, it is believed that transposition played a major evolutionary role in speciation by changing genome sizes and modifying gene expression patterns. For example, in bacteria, transposition can lead to conferring antibiotic resistance. Movement of transposable elements within the genetic pool of pathogenic bacteria can aid in transfer of antibiotic-resistant genetic elements. In eukaryotes, transposons can carry out...
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
Microbial Phylogeny01:28

Microbial Phylogeny

Understanding the evolutionary relationships among microorganisms is fundamental to microbial ecology and taxonomy. Phylogenetic trees are essential tools for inferring these relationships, relying primarily on comparative analyses of molecular sequences such as DNA, RNA, or proteins. In microbial studies, these trees typically depict the evolutionary paths of diverse bacterial and archaeal species by mapping genetic differences accumulated over time.Phylogenetic trees are composed of tips,...
Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
Phylogenetic Trees03:21

Phylogenetic Trees

Phylogenetic trees come in many forms. It matters in which sequence the organisms are arranged from the bottom to the top of the tree, but the branches can rotate at their nodes without altering the information. The lines connecting individual nodes can be straight, angled, or even curved.The length of the branches can depict time or the relative amount of change among organisms. For instance, the branch length might indicate the number of amino acid changes in the sequence that underlies the...

You might also read

Related Articles

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

Sort by
Same author

A Myocyte-Enriched Long Non-Coding RNA NRMLncR Enhances Myogenesis in Mouse.

FASEB journal : official publication of the Federation of American Societies for Experimental Biology·2026
Same author

Resident mesenchymal progenitor cells require autocrine IGF-I in homeostatic and regenerating skeletal muscle.

Stem cell reports·2026
Same author

Moderate iron restriction improves metabolism via epigenetic regulation of GDF15.

The Journal of nutritional biochemistry·2026
Same author

Integrated Genomic and Single-Cell Analysis Reveals Heterogeneity, Prognosis, and Treatment Vulnerability in Urothelial Carcinoma.

Human mutation·2026
Same author

Mitochondrial L-2-hydroxyglutarate is a physiological signalling metabolite.

Nature·2026
Same author

Chondrolectin regulates the sublaminar localization and regenerative function of muscle satellite cells in mice.

iScience·2026
Same journal

pGWAS-Portal: a comprehensive online platform for integrative post-genome-wide association study analysis.

BMC genomics·2026
Same journal

Physiological and transcriptomic analyses of Rosa persica in response to drought stress and functional validation of the transcription factor RpERF113-like.

BMC genomics·2026
Same journal

Integrated analysis of chromatin accessibility and transcriptome profiles in granulosa cells of sheep with different FecB genotypes.

BMC genomics·2026
Same journal

Correction: TB-DROP: deep learning-based drug resistance prediction of Mycobacterium tuberculosis utilizing whole genome mutations.

BMC genomics·2026
Same journal

Chromosomal scale genome assembly of medicinal plant Sophora tonkinensis.

BMC genomics·2026
Same journal

Variant-specific RNA testing resolves variants of uncertain significance in exome testing.

BMC genomics·2026
See all related articles

Related Experiment Video

Updated: Jun 29, 2026

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
08:57

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

Phylogenetic reconstruction from transpositions.

Feng Yue1, Meng Zhang, Jijun Tang

  • 1Department of Computer Science and Engineering, University of South Carolina, Columbia, SC 29208, USA. yuef@engr.sc.edu

BMC Genomics
|October 10, 2008
PubMed
Summary
This summary is machine-generated.

This study introduces GRAPPA-TP, a new computational method that accurately analyzes genome rearrangements, including transpositions. GRAPPA-TP improves phylogenetic reconstruction and ancestor genome inference, especially when transpositions are dominant.

More Related Videos

A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles
10:23

A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles

Published on: July 11, 2025

Genetic Mapping of Thermotolerance Differences Between Species of Saccharomyces Yeast via Genome-Wide Reciprocal Hemizygosity Analysis
10:08

Genetic Mapping of Thermotolerance Differences Between Species of Saccharomyces Yeast via Genome-Wide Reciprocal Hemizygosity Analysis

Published on: August 12, 2019

Related Experiment Videos

Last Updated: Jun 29, 2026

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
08:57

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles
10:23

A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles

Published on: July 11, 2025

Genetic Mapping of Thermotolerance Differences Between Species of Saccharomyces Yeast via Genome-Wide Reciprocal Hemizygosity Analysis
10:08

Genetic Mapping of Thermotolerance Differences Between Species of Saccharomyces Yeast via Genome-Wide Reciprocal Hemizygosity Analysis

Published on: August 12, 2019

Area of Science:

  • Computational Biology
  • Bioinformatics
  • Genomics

Background:

  • High-throughput sequencing enables whole-genome analysis.
  • Genome rearrangements are crucial for phylogenetic analysis.
  • Existing methods like GRAPPA and MGR primarily focus on inversions, struggling with transpositions.

Purpose of the Study:

  • To extend GRAPPA to effectively handle transpositions in genome rearrangement analysis.
  • To develop a new computational method for phylogenetic analysis incorporating transposition events.

Main Methods:

  • Developed GRAPPA-TP, extending the GRAPPA algorithm.
  • Implemented a heuristic method for estimating transposition distance.
  • Introduced a novel transposition median solver for analyzing three genomes.

Main Results:

  • GRAPPA-TP accurately estimates transposition distance, particularly for closely related genomes.
  • The method demonstrates high accuracy in ancestor genome inference and phylogenetic reconstruction.
  • Available at http://phylo.cse.sc.edu/.

Conclusions:

  • GRAPPA-TP significantly enhances genome rearrangement analysis by including transpositions.
  • Accurate phylogenetic reconstruction relies on appropriate model matching, specifically simulating transposition events correctly.
  • The study highlights the importance of considering all major rearrangement events for robust phylogenetic inference.