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Substitution Patterns Are Under Different Influences in Primates and Rodents

Summary: Substitution Patterns Are Under Different Influences in
Primates and Rodents
Yves Cle´ment* and Peter F. Arndt
Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
*Corresponding author: E-mail: clement@molgen.mpg.de.
Accepted: 11 February 2011
There are large-scale variations of the GC-content along mammalian chromosomes that have been called isochore
structures. Primates and rodents have different isochore structures, which suggests that these lineages exhibit different
modes of GC-content evolution. It has been shown that, in the human lineage, GC-biased gene conversion (gBGC), a neutral
process associated with meiotic recombination, acts on GC-content evolution by influencing A or T to G or C substitution
rates. We computed genome-wide substitution patterns in the mouse lineage from multiple alignments and compared them
with substitution patterns in the human lineage. We found that in the mouse lineage, gBGC is active but weaker than in the
human lineage and that male-specific recombination better predicts GC-content evolution than female-specific
recombination. Furthermore, we were able to show that G or C to A or T substitution rates are predicted by a combination
of different factors in both lineages. A or T to G or C substitution rates are most strongly predicted by meiotic recombination
in the human lineage but by CpG odds ratio (the observed CpG frequency normalized by the expected CpG frequency) in the
mouse lineage, suggesting that substitution patterns are under different influences in primates and rodents.
Key words: genome evolution, isochore, substitution patterns, meiotic recombination, biased gene conversion.


Source: Arndt, Peter - Max-Planck-Institut für molekulare Genetik
Spang, Rainer - Computational Molecular Biology Group, Max-Planck-Institut für molekulare Genetik


Collections: Biology and Medicine; Biotechnology; Computer Technologies and Information Sciences; Physics