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Related Experiment Videos

Codon usage by transposable elements and their host genes in five species.

Emmanuelle Lerat1, Pierre Capy, Christian Biémont

  • 1Laboratoire Biométrie et Biologie Evolutive, UMR CNRS 5558, Université Lyon 1, 69622 Villeurbanne Cedex, France.

Journal of Molecular Evolution
|April 20, 2002
PubMed
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Transposable elements (TEs) exhibit distinct codon usage patterns compared to host genes across diverse species. This AT-richness suggests selection constraints influence TE evolution, independent of host genomes.

Area of Science:

  • Genomics
  • Molecular Evolution
  • Bioinformatics

Background:

  • Transposable elements (TEs) are mobile genetic sequences within genomes.
  • Understanding TE codon usage provides insights into their evolution and interaction with host genomes.
  • Comparative genomics across species is crucial for identifying conserved and divergent evolutionary pressures.

Purpose of the Study:

  • To compare the codon usage patterns of transposable elements (TEs) with those of host genes.
  • To investigate whether codon usage differences are influenced by genome base composition or host-specific factors.
  • To determine if selection acts on TE codon usage.

Main Methods:

  • Factorial correspondence analysis (FCA) was employed to analyze codon usage.
  • Codon usage of TEs was compared to host genes in five model organisms: Drosophila melanogaster, Arabidopsis thaliana, Caenorhabditis elegans, Saccharomyces cerevisiae, and Homo sapiens.

Related Experiment Videos

  • Analysis focused on the distribution of AT content at different codon positions and in non-coding DNA.

    • Main Results:

    • TEs consistently showed higher AT-richness compared to host genes, irrespective of overall genome base composition.
    • A higher percentage of A + T at the third codon position in TEs, compared to the first, indicates selection constraints beyond mutational bias.
    • TE codon usage differed from the mean of host genes and, in some species, resembled that of weakly expressed genes, suggesting specific evolutionary pressures on TEs.

    Conclusions:

    • The AT-richness and specific codon usage of TEs are host-independent characteristics.
    • Selection acts on TE codon usage, implying functional or regulatory roles.
    • TEs may exhibit unique evolutionary behaviors within host genomes, influenced by selection pressures.