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Related Concept Videos

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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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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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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Other than maintaining genome stability via DNA repair, homologous recombination plays an important role in diversifying the genome. In fact, the recombination of sequences forms the molecular basis of genomic evolution. Random and non-random permutations of genomic sequences create a library of new amalgamated sequences. These newly formed genomes can determine the fitness and survival of cells. In bacteria, homologous and non-homologous types of recombination lead to the evolution of new...
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Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
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The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was  generated by gene duplication and divergence, indicating its critical role in evolution.
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Incomplete Lineage Sorting and Hybridization Statistics for Large-Scale Retroposon Insertion Data.

Andrej Kuritzin1, Tabea Kischka2,3, Jürgen Schmitz2

  • 1Department of System Analysis, Saint Petersburg State Institute of Technology, St. Petersburg, Russia.

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|March 12, 2016
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Summary

Ancient retroposon insertions offer reliable phylogenetic markers. New statistical models accurately analyze rare genomic changes, differentiating hybridization and lineage sorting for robust species ancestry reconstruction.

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Area of Science:

  • Genomics
  • Phylogenetics
  • Molecular Evolution

Background:

  • Ancient retroposon insertions are valuable phylogenetic markers due to their low homoplasy.
  • Accurate phylogenetic reconstruction relies on fixed, orthologous insertions, as polymorphic insertions can yield misleading results.

Purpose of the Study:

  • To develop novel statistical models for analyzing rare genomic changes (RGCs).
  • To differentiate conflicting phylogenetic signals arising from incomplete lineage sorting or ancestral hybridization.
  • To evaluate different genome data search strategies.

Main Methods:

  • Development of comprehensive statistical models for RGC pattern analysis.
  • Application of models to test and differentiate phylogenetic reconstructions.
  • Evaluation of significance thresholds for RGCs in phylogenetic inference.

Main Results:

  • Minimum RGCs required for significant phylogenetic support determined (e.g., 3 elements for equally screened species).
  • Models can distinguish between incomplete lineage sorting and ancestral hybridization based on RGC distribution.
  • A user-friendly R-application (KKSC insertion significance test) is provided.

Conclusions:

  • Novel statistical models enhance the reliability of phylogenetic reconstructions using RGCs.
  • The models provide a robust framework for analyzing complex evolutionary scenarios like hybridization.
  • The KKSC test facilitates the application of these advanced methods in evolutionary biology research.