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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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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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The evolution of new genes is critical for speciation. Exon recombination, also known as exon shuffling or domain shuffling, is an important means of new gene formation. It is observed across vertebrates, invertebrates, and in some plants such as potatoes and sunflowers. During exon recombination, exons from the same or different genes recombine and produce new exon-intron combinations, which might evolve into new genes. 
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Gene Conversion amongst Alu SINE Elements.

Liliya Doronina1, Olga Reising1, Jürgen Schmitz1,2

  • 1Institute of Experimental Pathology, ZMBE, University of Münster, 48149 Münster, Germany.

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|July 2, 2021
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Summary
This summary is machine-generated.

Gene conversion unifies repetitive DNA sequences like Alu elements in primates. This study identified 98 instances of Alu-Alu gene conversion, revealing hotspots and hybrid elements, offering new insights into transposable element evolution.

Keywords:
Alu subfamily conversiongene conversionhomoplasypartial gene conversiontransposable elements

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Area of Science:

  • Genomics
  • Molecular Evolution
  • Bioinformatics

Background:

  • Non-allelic gene conversion homogenizes homologous sequences during recombination, crucial for maintaining essential gene functions.
  • Transposable elements (TEs), particularly abundant Alu short interspersed elements (SINEs) in primate genomes, serve as substrates for gene conversion.
  • Gene conversion involving TEs can lead to functional domain duplications and complicate the annotation of orthologous elements across species.

Purpose of the Study:

  • To systematically investigate gene conversion events involving Alu elements in primate genomes.
  • To identify and characterize instances of Alu-Alu gene conversion and determine the directionality of the process.
  • To pinpoint hotspots of gene conversion activity within primate evolutionary history.

Main Methods:

  • Extraction and comparison of a large dataset (68,097) of Alu insertions across primate genomes.
  • Bioinformatic analysis to detect and classify Alu-Alu gene conversion events, including partial conversions.
  • Phylogenetic screening to identify evolutionary hotspots of gene conversion.

Main Results:

  • Discovery of 98 cases of Alu-Alu gene conversion, with directionality identified in 64 instances (e.g., AluS converting to AluY).
  • Identification of 69 cases of partial gene conversion, resulting in hybrid Alu elements.
  • Pinpointing three significant gene conversion hotspots in the ancestral lineages of Catarrhini, Hominoidea, and gibbons.

Conclusions:

  • The study provides a novel strategy for identifying post-integrative changes in transposable elements through systematic screening of primate loci.
  • Gene conversion is a significant force shaping the evolution and identity of Alu elements in primates.
  • The findings offer a new perspective on the dynamics of repetitive DNA and genome evolution.