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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 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.
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Non-LTR Retrotransposons03:18

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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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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 Retrotransposons03:08

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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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Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
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Related Experiment Video

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Efficient homology-based annotation of transposable elements using minimizers.

Laura Natalia Gonzalez-García1,2, Daniela Lozano-Arce1, Juan Pablo Londoño3

  • 1Systems and Computing Engineering Department Universidad de los Andes Bogotá Colombia.

Applications in Plant Sciences
|August 21, 2023
PubMed
Summary
This summary is machine-generated.

A new Next-Generation Sequencing Experience Platform (NGSEP) tool rapidly annotates transposable elements (TEs) in plant genomes. This method significantly speeds up the analysis of large, complex genomes, overcoming a key bottleneck in genome assembly.

Keywords:
bioinformaticsgenomicssoftwaretransposable elements

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Determination of the Optimal Chromosomal Locations for a DNA Element in Escherichia coli Using a Novel Transposon-mediated Approach
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Area of Science:

  • Genomics
  • Bioinformatics
  • Plant Science

Background:

  • Transposable elements (TEs) comprise over half of complex plant genomes and influence gene expression, impacting agronomically important traits.
  • Long-read sequencing enables assembly of large plant genomes, but transposable element annotation remains a significant challenge.

Purpose of the Study:

  • To introduce a novel functionality within the Next-Generation Sequencing Experience Platform (NGSEP) for efficient, homology-based transposable element annotation.
  • To address the bottleneck in transposable element annotation for large and complex plant genomes.

Main Methods:

  • Developed a new NGSEP feature that treats reference library sequences as long reads for mapping to genome assemblies.
  • Implemented a hierarchical annotation assignment based on homology to the reference library.
  • Evaluated the algorithm's performance on diverse plant species, including Arabidopsis thaliana, Oryza sativa, Coffea humblotiana, and Triticum aestivum.

Main Results:

  • The NGSEP functionality demonstrated superior speed compared to traditional homology-based annotation tools, achieving speedups of 3x to over 20x.
  • Reduced the annotation time for the bread wheat (Triticum aestivum) genome from months to hours.
  • Successfully recovered up to 80% of TEs annotated by RepeatMasker with a precision of up to 0.95.

Conclusions:

  • NGSEP provides a rapid and efficient solution for transposable element analysis, particularly in large and transposable element-rich plant genomes.
  • This advancement facilitates more comprehensive genome annotation and characterization in plants.