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Related Concept Videos

Overview of Transposition and Recombination02:13

Overview of Transposition and Recombination

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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...
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Genome Annotation and Assembly03:36

Genome Annotation and Assembly

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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.
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DNA-only Transposons02:57

DNA-only Transposons

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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...
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Transposons01:24

Transposons

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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...
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Non-LTR Retrotransposons03:18

Non-LTR Retrotransposons

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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...
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LTR Retrotransposons03:08

LTR Retrotransposons

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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...
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Related Experiment Video

Updated: Mar 26, 2026

Real-Time Quantification of the Effects of IS200/IS605 Family-Associated TnpB on Transposon Activity
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Accurate Transposable Element Annotation Is Vital When Analyzing New Genome Assemblies.

Roy N Platt1, Laura Blanco-Berdugo1, David A Ray2

  • 1Department of Biological Sciences, Texas Tech University.

Genome Biology and Evolution
|January 24, 2016
PubMed
Summary

Accurate transposable element (TE) annotation requires more than homology searches. Combining homology, de novo methods, and manual curation is essential for a complete understanding of genome-wide TE content.

Keywords:
Heliconius melpomeneHeterocephalus glaberMicrotus ochrogastergenome annotationtransposable elements

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Transposable elements (TEs) are mobile genetic sequences that can proliferate within genomes, sometimes comprising over half of the total DNA.
  • Identifying and annotating TEs is crucial for understanding genome evolution and function, especially in newly sequenced nonmodel organisms.

Discussion:

  • Simple homology-based TE identification methods are insufficient, particularly when phylogenetic distance increases.
  • Inaccurate annotations can arise from using suboptimal methods in TE identification and classification.
  • The accuracy of TE annotation is highly dependent on the chosen methodology.

Key Insights:

  • Combining homology-based and de novo repeat identification methods, alongside manual curation, significantly improves TE annotation accuracy.
  • Reannotation revealed a higher proportion of repetitive genomes and identified numerous new TE subfamilies, indicating recent TE activity.
  • Accurate TE landscape description necessitates integrated approaches, not solely reliance on homology.

Outlook:

  • Future genomic studies should adopt comprehensive TE annotation strategies to fully characterize repetitive elements.
  • Standardizing TE annotation pipelines will enhance comparability across diverse taxa.
  • Further research into the evolutionary dynamics of TEs will benefit from improved annotation techniques.