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Related Concept Videos

Overview of Transposition and Recombination02:13

Overview of Transposition and Recombination

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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Genetic Material

Within the human body, a complex and detailed system of trillions of cells works in unison to sustain life. Each cell houses a nucleus, which contains 46 chromosomes divided into 23 pairs. Chromosomes are highly coiled structures made of the genetic material DNA. These chromosomes are essential carriers of genetic information, with half inherited from the mother through her egg and the other half from the father's sperm, combining to create the unique genetic makeup of an individual.
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Non-LTR Retrotransposons

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 Retrotransposons

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Horizontal Gene Transfer01:27

Horizontal Gene Transfer

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Microarray-based Identification of Individual HERV Loci Expression: Application to Biomarker Discovery in Prostate Cancer
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The Gypsy Database (GyDB) of mobile genetic elements.

C Lloréns1, R Futami, D Bezemer

  • 1Biotech Vana, Valencia, Institut Cavanilles de Biodiversitat i Biología Evolutiva Universitat de València, Spain.

Nucleic Acids Research
|September 27, 2007
PubMed
Summary

The Gypsy Database (GyDB) classifies mobile genetic elements, focusing on Ty3/Gypsy and Retroviridae retroelements. Phylogenetic analysis of the gag-pro-pol region reveals evolutionary history, aiding in identifying new species.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Evolutionary Biology

Background:

  • Mobile genetic elements (MGEs) are crucial for genome evolution.
  • Ty3/Gypsy and Retroviridae long terminal repeat (LTR) retroelements are significant MGEs with complex evolutionary histories.
  • Current classification systems for these elements can be challenging due to redundancy and evolutionary divergence.

Purpose of the Study:

  • To introduce the Gypsy Database (GyDB), a novel resource for the non-redundant analysis and evolutionary classification of MGEs.
  • To present the initial version of GyDB, focusing on eukaryotic Ty3/Gypsy and Retroviridae LTR retroelements.
  • To establish a framework for classifying MGEs based on their evolutionary trajectories.

Main Methods:

  • Phylogenetic analyses were conducted using the gag-pro-pol internal region common to Ty3/Gypsy and Retroviridae.
  • Molecular profiles and phylogenies were generated for non-redundant analysis.
  • Existing classification systems (e.g., ICTV nomenclature, retroviral classes) were considered for validation.

Main Results:

  • Phylogenetic analyses strongly support previously described Ty3/Gypsy lineages based on reverse-transcriptase (RT) data.
  • Retroviridae formed monophyletic groups consistent with ICTV genera and established retroviral classes (I, II, III).
  • Protein domains within the gag-pro-pol region collectively reflect a shared evolutionary history for both element groups.

Conclusions:

  • The gag-pro-pol region provides a robust criterion for differentiating the molecular diversity of Ty3/Gypsy and Retroviridae.
  • GyDB offers a valuable, non-redundant resource for the evolutionary-based classification of MGEs.
  • The database facilitates the identification of new Ty3/Gypsy and Retroviridae species through comprehensive phylogenies and molecular profiles.