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Isochore evolution in mammals: a human-like ancestral structure

N Galtier1, D Mouchiroud

  • 1Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5558, Biométrie, Génétique et Biologie des Populations, Université Claude Bernard Lyon 1, 69622 Villeurbanne Cedex, France.

Genetics
|December 2, 1998
PubMed
Summary

Mammalian codon usage is shaped by genomic G + C-content, or isochore structure. Human-like ancestral G + C-content was inferred, suggesting mouse genomes evolved a more uniform structure.

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Area of Science:

  • Genomics
  • Molecular Evolution
  • Bioinformatics

Background:

  • Mammalian codon usage patterns are significantly influenced by genomic G + C-content, known as isochore structure.
  • Understanding the evolutionary history of isochore structure is crucial for deciphering genomic diversity in mammals.

Purpose of the Study:

  • To reconstruct the ancestral G + C-content at third codon positions in eutherian mammals.
  • To investigate the evolutionary trajectory of isochore structure, comparing ancestral states with extant species like mice.

Main Methods:

  • Utilized maximum-likelihood analysis to estimate ancestral G + C-content.
  • Employed a nonhomogeneous DNA substitution model accounting for variable base compositions.
  • Analyzed 27 nuclear protein-coding genes from eutherian mammals.

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Main Results:

  • Results consistently supported a human-like ancestral pattern of highly variable G + C-content across genes.
  • The narrower G + C-content distribution observed in mouse genomes is likely a derived characteristic.
  • Isochore evolution in mammals suggests a potential link between G + C-content homogenization and mutation rates.

Conclusions:

  • The ancestral mammalian genome likely exhibited heterogeneous G + C-content, similar to humans.
  • Murid (mouse) genomes represent a derived state with homogenized G + C-content.
  • Homogenization may be linked to high mutation rates and negative selection pressures on isochore maintenance.