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

16.3K
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...
16.3K
DNA-only Transposons02:57

DNA-only Transposons

15.8K
DNA-only transposons are called autonomous transposons since they code for the enzyme transposase that is required for the transposition mechanism. Insertion of transposons can alter gene functions in multiple ways. They can mutate the gene, alter gene expression by introducing a novel promoter or insulator sequence, introduce new splice sites, and change the mRNA transcripts produced, or remodel chromatin structure.
The donor site from where the transposon is excised is either degraded or...
15.8K
Transposons01:24

Transposons

3.2K
Transposons, or "jumping genes," are small mobile genetic elements (MGEs) that range from 700 to 40,000 base pairs in length. They are found in all organisms and can move within the same chromosome or transfer to different chromosomes. In some cases, transposons can also jump between different host DNA molecules, such as plasmids or viruses, contributing to genetic variability.Barbara McClintock first discovered these mobile genetic elements in the 1940s while studying maize genetics, and she...
3.2K
Non-LTR Retrotransposons03:18

Non-LTR Retrotransposons

12.4K
As the name suggests, non-LTR retrotransposons lack the long terminal repeats characteristic of the LTR retrotransposons. Additionally, both LTR and non-LTR retrotransposons use distinct mechanisms of mobilization. Non-LTR retrotransposons are further divided into two classes - Long interspersed nuclear elements (LINEs) and short interspersed nuclear elements (SINEs), both of which occur abundantly in most mammals, including humans. Some of the active non-LTR retrotransposons in humans are L1...
12.4K
LTR Retrotransposons03:08

LTR Retrotransposons

18.0K
LTR retrotransposons are class I transposable elements with long terminal repeats flanking an internal coding region. These elements are less abundant in mammals compared to other class I transposable elements. About 8 percent of human genomic DNA comprises LTR retrotransposons. Some of the common examples of LTR retrotransposons are Ty elements in yeast and Copia elements in Drosophila.
The internal coding region of LTR retrotransposons and their mechanism of transposition closely resembles a...
18.0K
Genome Annotation and Assembly03:36

Genome Annotation and Assembly

16.7K
The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
16.7K

You might also read

Related Articles

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

Sort by
Same author

The tiny germline chromosomes of Paramecium aurelia have an exceptionally high recombination rate and are capped by a new class of Helitrons.

BMC biology·2026
Same author

A reference-free pipeline for detecting shared transposable elements from pan-genomes to retrace their dynamics in a species.

Genome biology·2026
Same author

Pathogenic and Genetic Diversity of <i>Sclerotium rolfsii,</i> the Causal Agent of Southern Blight of Common Bean in Uganda.

Journal of fungi (Basel, Switzerland)·2026
Same author

Chromosome Structure of Wild Wheat Relative <italic>Aegilops uniaristata</italic>.

Cytogenetic and genome research·2026
Same author

The Evolution and Origin of Allotetraploid Aegilops geniculata Revealed by the Homoeolog-Resolved Genome Assembly.

Plant biotechnology journal·2025
Same author

Interchromosomal linkage disequilibrium analysis reveals strong indications of sign epistasis in wheat breeding families.

G3 (Bethesda, Md.)·2025
Same journal

3DICE: Interpretable 3D Cross-Modal Learning for Drug-Target Interaction Prediction and Large-Scale Drug Discovery.

Bioinformatics (Oxford, England)·2026
Same journal

KASSPer: Kinase Active Site Structure Prediction using Protein and Ligand Language Models and Its Application to Virtual Screening.

Bioinformatics (Oxford, England)·2026
Same journal

IDR searcher: a search engine solution for public image resources.

Bioinformatics (Oxford, England)·2026
Same journal

KCFtools: Rapid alignment-free method for introgression screening and GWAS using k-mer profiles.

Bioinformatics (Oxford, England)·2026
Same journal

Meta2DB: Curated shotgun metagenomic feature sets and metadata for health state prediction.

Bioinformatics (Oxford, England)·2026
Same journal

conMItion: an R package adjusting confounding factors for associations in multi-omics.

Bioinformatics (Oxford, England)·2026
See all related articles

Related Experiment Video

Updated: Apr 28, 2026

Novel Sequence Discovery by Subtractive Genomics
09:40

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

7.7K

Tedna: a transposable element de novo assembler.

Matthias Zytnicki1, Eduard Akhunov1, Hadi Quesneville1

  • 1INRA, URGI, Plant Breeding and Biology, Versailles 78026, France and Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA.

Bioinformatics (Oxford, England)
|June 5, 2014
PubMed
Summary
This summary is machine-generated.

Tedna is a new de novo assembler for transposable elements, designed to work with Illumina paired-end reads. This tool effectively reconstructs full-length transposable elements, improving genome assembly accuracy.

More Related Videos

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved Non-model Organisms
10:41

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved Non-model Organisms

Published on: May 9, 2017

9.9K
Use of Alu Element Containing Minigenes to Analyze Circular RNAs
13:10

Use of Alu Element Containing Minigenes to Analyze Circular RNAs

Published on: March 10, 2020

6.9K

Related Experiment Videos

Last Updated: Apr 28, 2026

Novel Sequence Discovery by Subtractive Genomics
09:40

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

7.7K
Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved Non-model Organisms
10:41

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved Non-model Organisms

Published on: May 9, 2017

9.9K
Use of Alu Element Containing Minigenes to Analyze Circular RNAs
13:10

Use of Alu Element Containing Minigenes to Analyze Circular RNAs

Published on: March 10, 2020

6.9K

Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Genome sequencing is advancing, but de novo assemblers struggle with repetitive genomic regions.
  • Transposable elements (TEs) are crucial for genome diversity and adaptation, yet are often poorly assembled.
  • Existing TE assemblers are limited to small genomes or older sequencing technologies.

Purpose of the Study:

  • To develop a novel de novo assembler for transposable elements.
  • To enable the assembly of full-length transposable elements from modern sequencing data.

Main Methods:

  • Tedna utilizes Illumina paired-end reads for de novo assembly.
  • The assembler is implemented in C++11 and requires the Sparsehash Package.
  • Tedna is designed for efficient use on standard computers with parallelized code.

Main Results:

  • Tedna successfully assembles a set of transposable elements directly from sequencing reads.
  • The tool forms full-length transposable elements, addressing limitations of previous assemblers.
  • Tedna is capable of handling genomes with high proportions of transposable elements.

Conclusions:

  • Tedna offers an improved solution for de novo assembly of transposable elements.
  • The tool enhances the accuracy of genome assembly, particularly in repetitive regions.
  • Tedna supports current sequencing technologies and is accessible for broad laboratory use.