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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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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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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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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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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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Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

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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...
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Related Experiment Video

Updated: Aug 19, 2025

Determination of the Optimal Chromosomal Locations for a DNA Element in Escherichia coli Using a Novel Transposon-mediated Approach
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An Overview of Best Practices for Transposable Element Identification, Classification, and Annotation in Eukaryotic

Fernando Rodriguez1, Irina R Arkhipova2

  • 1Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, USA. frodriguez@mbl.edu.

Methods in Molecular Biology (Clifton, N.J.)
|November 30, 2022
PubMed
Summary

Transposable elements (TEs) are mobile genetic sequences impacting eukaryotic genomes. This study provides practical guidance for accurately identifying and annotating TEs in non-model organisms, improving mobilome descriptions.

Keywords:
Consensus sequencesDNA transposonsDe novo repeat identificationManual curationRepeat libraryRepetitive DNARetrotransposons

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Area of Science:

  • Genomics
  • Molecular Biology
  • Evolutionary Biology

Background:

  • Transposable elements (TEs) significantly influence eukaryotic genome structure, function, and evolution.
  • Advancements in multi-omics data enable new model organisms for biological research.
  • However, TE identification and annotation lag behind host gene annotation standards.

Purpose of the Study:

  • To provide comprehensive mobilome descriptions for genome projects.
  • To improve TE boundary designation, reduce identification errors, and ensure accurate insertion information.
  • To offer practical advice and step-by-step instructions for TE annotation in non-model organisms.

Main Methods:

  • Developing practical advice for generating TE models in de novo assemblies.
  • Providing step-by-step instructions for commonly used TE analysis pipelines.
  • Suggesting improvements for TE analysis tools.

Main Results:

  • The study offers practical strategies for TE identification and annotation.
  • It guides inexperienced researchers through TE analysis workflows.
  • It highlights areas for improvement in existing TE annotation tools.

Conclusions:

  • Accurate TE annotation is crucial for understanding eukaryotic genomes.
  • Standardized and improved TE annotation methods are needed for non-model organisms.
  • This work aims to enhance the study of mobilomes across diverse species.