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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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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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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.
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A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
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Efficient Detection of Transposable Element Insertion Polymorphisms Between Genomes Using Short-Read Sequencing Data.

Pierre Baduel1, Leandro Quadrana2, Vincent Colot3

  • 1Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Ecole Normale Supérieure, PSL Research University, Paris, France.

Methods in Molecular Biology (Clifton, N.J.)
|April 26, 2021
PubMed
Summary
This summary is machine-generated.

Transposable elements (TEs) cause mutations, but detecting these insertion polymorphisms (TIPs) in new genomes is challenging. Our new bioinformatic framework accurately identifies TE variants in non-reference genomes using short-read data.

Keywords:
TE insertion polymorphismTransposable element

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Area of Science:

  • Genomics
  • Bioinformatics
  • Population Genetics

Background:

  • Transposable elements (TEs) are mobile DNA sequences that can cause significant mutations.
  • Most TE-induced mutations are detrimental and exist at low frequencies, making them hard to detect.
  • Existing reference genomes capture only a small fraction of TE insertion polymorphisms (TIPs).

Purpose of the Study:

  • To develop and validate a robust bioinformatic framework for detecting TE insertion polymorphisms (TIPs).
  • To identify both non-reference TE presence and reference TE absence variants.
  • To assess the performance of the developed method on multiple non-reference genomes.

Main Methods:

  • Combined improved SPLITREADER and TEPID pipelines for TE variant detection.
  • Utilized short-read sequencing data from ten non-reference Arabidopsis thaliana genomes.
  • Benchmarked the framework for specificity and sensitivity in TIP detection.

Main Results:

  • The bioinformatic framework successfully detected non-reference TE presence and reference TE absence variants.
  • High specificity and sensitivity were demonstrated in TIP detection across ten genomes.
  • The method effectively leverages widely available short-read sequencing data.

Conclusions:

  • The developed framework provides a sensitive and specific method for identifying TE insertion polymorphisms.
  • This tool enhances the ability to study TE dynamics in non-reference genomes.
  • Facilitates a deeper understanding of TE-driven evolution and its impact on species.