title: Paleogenomics or the search for remnant duplicated copies of the yeast DUP240 gene family in intergenic areas.
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-open reading frames (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 nondegenerate 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 because the possibility of finding short conserved protein motifs in intergenic regions (IRs) largely depends on the choice of the most closely related paralog or ortholog. By mapping new genetic components in previously annotated IRs, our study 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.
authors.affiliation: Laboratoire de Dynamique, Evolution et Expression de Génomes de Microorganismes, FRE 2326 ULP/CNRS, Institut de Botanique, Strasbourg, France.
authors.forename: Bénédicte
authors.initials: B
authors.lastname: Wirth
authors.forename: Véronique Leh
authors.initials: VL
authors.lastname: Louis
authors.forename: Serge
authors.initials: S
authors.lastname: Potier
authors.forename: Jean-Luc
authors.initials: JL
authors.lastname: Souciet
authors.forename: Laurence
authors.initials: L
authors.lastname: Despons
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D021901:DNA, Intergenic / Q000235:genetics* / Q000266:history; D019143:Evolution, Molecular; D020440:Gene Duplication; D016681:Genome, Fungal; D049690:History, Ancient; D008969:Molecular Sequence Data; D005810:Multigene Family / Q000235:genetics*; D016366:Open Reading Frames; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics*; D017422:Sequence Analysis, DNA; D020080:Tandem Repeat Sequences
chemical_list: D021901:DNA, Intergenic; D029701:Saccharomyces cerevisiae Proteins