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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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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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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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Large-Scale Identification of Transposon Insertion Polymorphisms in Leguminous Plants from Paired-End WGS Data.

Ayushman Kumar Banerjee1,2, Mukesh Jain2, Rohini Garg3

  • 1Department of Life Sciences, School of Natural Sciences, Shiv Nadar Institution of Eminence, Gautam Buddha Nagar, Uttar Pradesh, India.

Methods in Molecular Biology (Clifton, N.J.)
|October 1, 2025
PubMed
Summary

This study introduces a bioinformatics method to identify transposon insertion polymorphisms (TIPs) in plants using whole-genome sequencing. This approach aids in understanding how transposable elements (TEs) drive genome evolution and impact crop traits.

Keywords:
Genome evolutionTransposable ElementsTransposon Insertion PolymorphismsWhole Genome Sequencing

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Area of Science:

  • Genomics
  • Bioinformatics
  • Plant Science

Background:

  • Transposable elements (TEs) are mobile DNA sequences that shape genome structure and evolution.
  • Understanding TE dynamics is crucial for deciphering genetic diversity and phenotypic variation, particularly in plants.
  • TEs play significant roles in genome evolution and the development of agronomic traits.

Purpose of the Study:

  • To provide a detailed bioinformatics protocol for identifying transposon insertion polymorphisms (TIPs) from paired-end whole-genome sequencing data.
  • To establish a robust and scalable framework for studying TE-driven genome evolution in plants.
  • To facilitate research into the contribution of TEs to agronomic trait development.

Main Methods:

  • Utilizing paired-end whole-genome sequencing data.
  • Applying computational pipelines and validated methodologies for TE identification.
  • Leveraging the TRACKPOSON tool and complementary bioinformatics resources.

Main Results:

  • Systematic identification and characterization of genomic TEs.
  • Quantification of transposon insertion polymorphisms (TIPs) in plant genomes.
  • Development of a robust framework for analyzing TE-mediated genome evolution.

Conclusions:

  • The presented bioinformatics approach enables effective identification and characterization of TEs and TIPs in plants.
  • This methodology offers critical insights for both foundational research and translational applications in plant breeding.
  • The protocol supports the study of TE roles in genome evolution and agronomic trait development, including in legumes.