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Genome Biology and Evolution Advance Access originally published online on April 30, 2009
Genome Biology and Evolution (2009) Vol. 2009:56; doi:10.1093/gbe/evp006 published on May 22, 2009
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© 2009 The Authors
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Footprints of Inversions at Present and Past Pseudoautosomal Boundaries in Human Sex Chromosomes

Claire Lemaitre1,2, Marilia D. V. Braga1,3, Christian Gautier, Marie-France Sagot, Eric Tannier and Gabriel A. B. Marais

Université de Lyon; Université Lyon 1; Centre National de la Recherche Scientifique; Institut National de Recherche en Informatique et en Automatique; UMR5558; Laboratoire de Biométrie et Biologie évolutive; Villeurbanne, F-69622 cedex, France

E-mail: marais{at}biomserv.univ-lyon1.fr, Eric.Tannier{at}inria.fr.


  Abstract

The human sex chromosomes have stopped recombining gradually, which has left five evolutionary strata on the X chromosome. Y inversions are thought to have suppressed X–Y recombination but clear evidence is missing. Here, we looked for such evidence by focusing on a region—the X-added region (XAR)—that includes the pseudoautosomal region and the most recent strata 3 to 5. We estimated and analyzed the whole set of parsimonious scenarios of Y inversions given the gene order in XAR and its Y homolog. Comparing these to scenarios for simulated sequences suggests that the strata 4 and 5 were formed by Y inversions. By comparing the X and Y DNA sequences, we found clear evidence of two Y inversions associated with duplications that coincide with the boundaries of strata 4 and 5. Divergence between duplicates is in agreement with the timing of strata 4 and 5 formation. These duplicates show a complex pattern of gene conversion that resembles the pattern previously found for AMELXY, a stratum 3 locus. This suggests that this locus—despite AMELY being unbroken—was possibly involved in a Y inversion that formed stratum 3. However, no clear evidence supporting the formation of stratum 3 by a Y inversion was found, probably because this stratum is too old for such an inversion to be detectable. Our results strongly support the view that the most recent human strata have arisen by Y inversions and suggest that inversions have played a major role in the differentiation of our sex chromosomes.

Keywords: inversion, duplication, recombination, sex chromosomes, evolutionary strata

Accepted April 12, 2009

1 Equal contribution to this work.

2 Present address: Université de Bordeaux, Centre de Bioinformatique–Génomique Fonctionnelle Bordeaux, Bordeaux, France.

3 Present address: Universität Bielefeld, Technische Fakultät, AG Genominformatik, Bielefeld, Germany.

Kateryna Makova, Associate Editor


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