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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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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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DNA-only Transposons02:57

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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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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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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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Reversal and Transposition Distance on Unbalanced Genomes Using Intergenic Information.

Alexsandro Oliveira Alexandrino1, Andre Rodrigues Oliveira2, Géraldine Jean3

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Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
|May 24, 2023
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Summary
This summary is machine-generated.

This study introduces a new algorithm for calculating genome rearrangement distance, improving efficiency for unbalanced genomes by incorporating intergenic information and handling insertions/deletions. The algorithm achieves a 4-approximation factor for complex genomic rearrangements.

Keywords:
indelsintergenic regionsreversalstranspositions

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Traditional genome rearrangement distance calculations assume identical gene content.
  • Recent advances allow for unbalanced genomes and incorporate genomic features like intergenic region sizes.

Purpose of the Study:

  • To develop and analyze algorithms for calculating genome rearrangement distances (Reversal, Transposition, Indel) on unbalanced genomes using intergenic information.
  • To improve approximation factors for transpositions and indels on unbalanced genomes.

Main Methods:

  • Developed a 4-approximation algorithm for Reversal, Transposition, and Indel (Insertion and Deletion) Distance on unbalanced genomes.
  • Extended the algorithm to include gene orientation, maintaining the 4-approximation factor.
  • Evaluated algorithm performance using simulated genomic data.

Main Results:

  • Achieved a 4-approximation algorithm for transposition and indel distances on unbalanced genomes, improving upon a previous 4.5 approximation.
  • Successfully extended the algorithm to account for gene orientation while preserving the approximation factor.
  • Demonstrated the practical applicability of the algorithms through experimental evaluation on simulated datasets.

Conclusions:

  • The proposed algorithms provide efficient and accurate methods for calculating genome rearrangement distances on unbalanced genomes, incorporating intergenic information and gene orientation.
  • These advancements enhance our ability to compare genomes with differing gene content and complex structural variations.
  • The study contributes to the field of comparative genomics by offering improved computational tools for evolutionary analysis.