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LTR Retrotransposons

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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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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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Viral genomes exhibit remarkable diversity in size, structure, and composition, influencing their replication strategies and interactions with host cells. These genomes consist of either DNA or RNA and may be linear or circular. Additionally, they can be single-stranded or double-stranded, with each configuration affecting how the virus propagates within a host. RNA viruses, for instance, generally have smaller genomes than DNA viruses, a factor that contributes to their high mutation rates and...
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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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Horizontal gene transfer (HGT) is a process where genetic material moves between organisms within the same generation, unlike vertical gene transfer, which occurs from parent to offspring. HGT plays a crucial role in microbial evolution, adaptation, and survival, particularly in shared environments like the human gut.Mobile genetic elements such as plasmids, prophages, integrons, insertion sequences, and transposons facilitate this process. HGT occurs through three primary mechanisms:...
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The basic reaction of homologous recombination (HR) involves two chromatids that contain DNA sequences sharing a significant stretch of identity. One of these sequences uses a strand from another as a template to synthesize DNA in an enzyme-catalyzed reaction. The final product is a novel amalgamation of the two substrates. To ensure an accurate recombination of sequences, HR is restricted to the S and G2 phases of the cell cycle. At these stages, the DNA has been replicated already and the...
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WgLink: reconstructing whole-genome viral haplotypes using L0+L1-regularization.

Chen Cao1, Matthew Greenberg2, Quan Long1,2,3

  • 1Department of Biochemistry and Molecular Biology, Alberta Children's Hospital Research Institute, Calgary, AB, T2N 4N1 Canada.

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Summary

WgLink improves viral genome reconstruction by patching together local sequences into whole genomes. This novel method offers higher accuracy and reduced computational resource usage compared to existing tools.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Next-generation sequencing (NGS) enables viral sequence reconstruction.
  • Existing tools struggle with whole viral genome (strain) reconstruction, especially with high coverage or large genomes.
  • Current methods often consume significant memory and computational resources.

Purpose of the Study:

  • To develop a novel computational tool, WgLink, for accurate and efficient whole viral genome reconstruction.
  • To address the limitations of existing tools in assembling complete viral strains from NGS data.
  • To improve the accuracy and reduce the resource consumption of viral genome assembly.

Main Methods:

  • WgLink takes local sequence reconstructions as input.
  • It employs L0+L1-regularized regression to integrate variant allele frequency data with physical linkage information.
  • The method simultaneously analyzes multiple variants across multiple regions to achieve whole-genome assembly.

Main Results:

  • WgLink demonstrates higher accuracy in reconstructing whole viral genomes compared to existing tools.
  • The tool was validated on both simulated and real viral sequencing datasets.
  • WgLink significantly reduces memory (RAM) and CPU time requirements.

Conclusions:

  • WgLink effectively reconstructs complete viral genomes (strains) from NGS data.
  • The tool overcomes limitations of existing methods in accuracy and resource efficiency.
  • WgLink offers a promising solution for large-scale viral genomics and surveillance.