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

15.2K
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...
15.2K
DNA-only Transposons02:57

DNA-only Transposons

14.3K
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...
14.3K
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

5.7K
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...
5.7K
Non-LTR Retrotransposons03:18

Non-LTR Retrotransposons

11.4K
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...
11.4K
LTR Retrotransposons03:08

LTR Retrotransposons

17.3K
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...
17.3K
Export of Mitochondrial and Chloroplast Genes02:19

Export of Mitochondrial and Chloroplast Genes

3.6K
A eukaryotic cell can have up to three different types of genetic systems: nuclear, mitochondrial, and chloroplast. During evolution, organelles have exported many genes to the nucleus; this transfer is still ongoing in some plant species. Approximately 18% of the Arabidopsis thaliana nuclear genome is thought to be derived from the chloroplast’s cyanobacterial ancestor, and around 75% of the yeast genome derived from the mitochondria’s bacterial ancestor. This export has occurred...
3.6K

You might also read

Related Articles

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

Sort by
Same author

A new phased assembly of the Antarctic spiny plunderfish provides novel insights into the evolution of the notothenioid radiation.

bioRxiv : the preprint server for biology·2026
Same author

Cryptic Diversity and Impacts of Domestication in the Black Soldier Fly (Hermetia illucens) Genome.

Genome biology and evolution·2026
Same author

Transgenerational effects of heat shock on gene regulation and fitness-related traits in natural Drosophila populations.

Molecular biology and evolution·2026
Same author

The Genomics of Convergent Adaptation to Intertidal Gravel Beaches in Mediterranean Clingfishes.

Genome biology and evolution·2026
Same author

FastGA: fast genome alignment.

Bioinformatics advances·2025
Same author

Continent-wide differentiation of fitness traits and patterns of climate adaptation among European populations of <i>Drosophila melanogaster</i>.

Evolution letters·2025

Related Experiment Video

Updated: Jun 5, 2025

Identification of Functionally-Relevant Lentivirus Integration Sites in an Insertional Mutagenesis Cell Library
07:28

Identification of Functionally-Relevant Lentivirus Integration Sites in an Insertional Mutagenesis Cell Library

Published on: January 10, 2025

224

MCHelper automatically curates transposable element libraries across eukaryotic species.

Simon Orozco-Arias1, Pío Sierra2, Richard Durbin2

  • 1Institute of Evolutionary Biology, CSIC, UPF, 08003 Barcelona, Spain.

Genome Research
|December 9, 2024
PubMed
Summary

Automating transposable element (TE) library curation with MCHelper significantly improves genome annotation quality. This tool reduces redundancy and false positives, making large-scale genomic studies more efficient and reproducible.

More Related Videos

Robust DNA Isolation and High-throughput Sequencing Library Construction for Herbarium Specimens
13:03

Robust DNA Isolation and High-throughput Sequencing Library Construction for Herbarium Specimens

Published on: March 8, 2018

10.5K
HOX Loci Focused CRISPR/sgRNA Library Screening Identifying Critical CTCF Boundaries
10:10

HOX Loci Focused CRISPR/sgRNA Library Screening Identifying Critical CTCF Boundaries

Published on: March 31, 2019

8.3K

Related Experiment Videos

Last Updated: Jun 5, 2025

Identification of Functionally-Relevant Lentivirus Integration Sites in an Insertional Mutagenesis Cell Library
07:28

Identification of Functionally-Relevant Lentivirus Integration Sites in an Insertional Mutagenesis Cell Library

Published on: January 10, 2025

224
Robust DNA Isolation and High-throughput Sequencing Library Construction for Herbarium Specimens
13:03

Robust DNA Isolation and High-throughput Sequencing Library Construction for Herbarium Specimens

Published on: March 8, 2018

10.5K
HOX Loci Focused CRISPR/sgRNA Library Screening Identifying Critical CTCF Boundaries
10:10

HOX Loci Focused CRISPR/sgRNA Library Screening Identifying Critical CTCF Boundaries

Published on: March 31, 2019

8.3K

Area of Science:

  • Genomics
  • Bioinformatics
  • Evolutionary Biology

Background:

  • The increasing number of high-quality genome sequences necessitates accurate annotation of both genic and transposable element (TE) sequences.
  • Transposable elements play crucial roles in genome evolution, gene regulation, and host trait development.
  • Current de novo TE identification tools require manual curation, which is time-consuming, lacks reproducibility, and is impractical for large-scale projects.

Purpose of the Study:

  • To develop and evaluate MCHelper, a tool designed to automate the curation of transposable element libraries.
  • To assess the impact of automated curation on the quality of TE libraries and genome annotations across diverse species.

Main Methods:

  • MCHelper was utilized in its fully automated mode.
  • Outputs from three de novo TE identification tools (RepeatModeler2, EDTA, REPET) were processed using MCHelper.
  • The study involved analysis of genomes from fruit fly, rice, hooded crow, zebrafish, maize, and human.

Main Results:

  • MCHelper significantly improved the quality of TE libraries, reducing consensus sequences by up to 65% and false positives by up to 11.4%.
  • The proportion of "unclassified/unknown" TE consensus sequences was reduced by approximately 48%.
  • Genome-wide TE annotations showed improvements, including the identification of larger, unfragmented TE insertions.

Conclusions:

  • MCHelper provides a fully automated and efficient solution for transposable element library curation.
  • The tool enhances the accuracy and reduces redundancy in TE annotations, facilitating large-scale genomic analyses.
  • MCHelper is easy to install and use, offering a valuable resource for the genomics community.