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MBE Advance Access published online on May 25, 2005
Molecular Biology and Evolution, doi:10.1093/molbev/msi170
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Published by Oxford University Press 2005.
Accepted May 12, 2005

Research Article

Paleogenomics or the Search for Remnant Duplicated Copies of the Yeast DUP240 Gene Family in Intergenic Areas

Bénédicte Wirth 1, Véronique Leh Louis 1, Serge Potier 1, Jean-Luc Souciet 1*, and Laurence Despons 1

1 Laboratoire de Dynamique, Evolution et Expression des Génomes de Micro-Organismes, FRE 2326 ULP/CNRS, Institut de Botanique, 28 rue Goethe, F-67083 Strasbourg Cedex, France

* To whom correspondence should be addressed.
Jean-Luc Souciet, E-mail: souciet{at}gem.u-strasbg.fr


  Abstract

Duplication, resulting in gene redundancy, is well known to be a driving force of evolutionary change. Gene families are therefore useful targets for approaching genome evolution. To address the gene death process we examined the fate of the 10-member large S288C DUP240 family in 15 Saccharomyces cerevisiae strains. Using an original three-step method of analysis reported here, both slightly and highly degenerate DUP240 copies, called pseudo-ORFs and relics, respectively, were detected in strain S288C. It was concluded that two previously annotated ORFs correspond in fact to pseudo-ORFs, and three additional relics were identified in intergenic areas. Comparative intraspecies analysis of these degenerate DUP240 loci revealed that the two pseudo-ORFs are present in a non-degenerate state in some other strains. This suggests that within a given gene family, different loci are the target of the gene erasure process, which is therefore strain dependent. Besides, the variable positions observed indicate that the relic sequence may diverge faster than the flanking regions. All in all, this study shows that short conserved protein motifs provide a useful tool for detecting and accurately mapping degenerate gene remnants. The present results also highlight the strong contribution of comparative genomics for gene relic detection, since the possibility of finding short conserved protein motifs in intergenic regions largely depends on the choice of the most closely related paralog or ortholog. By mapping new genetic components in previously annotated intergenic regions, our study therefore constitutes a further refinement step in the crucial stage of genome annotation, and provides a strategy for retracing ancient chromosomal reshaping events and hence, for deciphering genome history.

Keywords: DUP240 family; fate of duplicated genes; gene death; pseudogenes; relics; Saccharomyces cerevisiae.
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