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Originally published as Genetics Published Articles Ahead of Print on June 22, 2009.

Genetics, Vol. 183, 31-38, September 2009, Copyright © 2009
doi:10.1534/genetics.109.105049

GC Content and Recombination: Reassessing the Causal Effects for the Saccharomyces cerevisiae Genome

Marie-Claude Marsolier-Kergoat*,1 and Edouard Yeramian{dagger}

* Institut de Biologie et de Technologies de Saclay, Commissariat à l'Energie Atomique/Saclay, 91191 Gif-sur-Yvette, France and {dagger} Unité de Bio-Informatique Structurale, Centre National de la Recherche Scientifique Unité de Recherche Associée 2185, Institut Pasteur, 75724 Paris, France

1 Corresponding author: Institut de Biologie et de Technologies de Saclay, Service de Biologie Intégrative et de Génétique Moléculaire, Bât. 144, CEA/Saclay, 91191 Gif-sur-Yvette Cedex, France.
E-mail: mcmk{at}cea.fr

Recombination plays a crucial role in the evolution of genomes. Among many chromosomal features, GC content is one of the most prominent variables that appear to be highly correlated with recombination. However, it is not yet clear (1) whether recombination drives GC content (as proposed, for example, in the biased gene conversion model) or the converse and (2) what are the length scales for mutual influences between GC content and recombination. Here we have reassessed these questions for the model genome Saccharomyces cerevisiae, for which the most refined recombination data are available. First, we confirmed a strong correlation between recombination rate and GC content at local scales (a few kilobases). Second, on the basis of alignments between S. cerevisiae, S. paradoxus, and S. mikatae sequences, we showed that the inferred AT/GC substitution patterns are not correlated with recombination, indicating that GC content is not driven by recombination in yeast. These results thus suggest that, in S. cerevisiae, recombination is determined either by the GC content or by a third parameter, also affecting the GC content. Third, we observed long-range correlations between GC and recombination for chromosome III (for which such correlations were reported experimentally and were the model for many structural studies). However, similar correlations were not detected in the other chromosomes, restraining thus the generality of the phenomenon. These results pave the way for further analyses aimed at the detailed untangling of drives involved in the evolutionary shaping of the yeast genome.