title: Variation in gene duplicates with low synonymous divergence in Saccharomyces cerevisiae relative to Caenorhabditis elegans.
abstract: BACKGROUND
  The direct examination of large, unbiased samples of young gene duplicates in their early stages of evolution is crucial to understanding the origin, divergence and preservation of new genes. Furthermore, comparative analysis of multiple genomes is necessary to determine whether patterns of gene duplication can be generalized across diverse lineages or are species-specific. Here we present results from an analysis comprising 68 duplication events in the Saccharomyces cerevisiae genome. We partition the yeast duplicates into ohnologs (generated by a whole-genome duplication) and non-ohnologs (from small-scale duplication events) to determine whether their disparate origins commit them to divergent evolutionary trajectories and genomic attributes.
  
  
  RESULTS
  We conclude that, for the most part, ohnologs tend to appear remarkably similar to non-ohnologs in their structural attributes (specifically the relative composition frequencies of complete, partial and chimeric duplicates), the discernible length of the duplicated region (duplication span) as well as genomic location. Furthermore, we find notable differences in the features of S. cerevisiae gene duplicates relative to those of another eukaryote, Caenorhabditis elegans, with respect to chromosomal location, extent of duplication and the relative frequencies of complete, partial and chimeric duplications.
  
  
  CONCLUSIONS
  We conclude that the variation between yeast and worm duplicates can be attributed to differing mechanisms of duplication in conjunction with the varying efficacy of natural selection in these two genomes as dictated by their disparate effective population sizes.
authors: Department of Biology, Castetter Hall, 1 University of New Mexico, Albuquerque, NM 87131-0001, USA. vkatju@unm.edu
authors: Vaishali
authors: V
authors: Katju
authors: James C
authors: JC
authors: Farslow
authors: Ulfar
authors: U
authors: Bergthorsson
mesh_terms: D000818:Animals; D017173:Caenorhabditis elegans / Q000235:genetics*; D002874:Chromosome Mapping; D015825:Chromosomes, Fungal / Q000235:genetics; D019295:Computational Biology / Q000379:methods; D005656:Fungal Proteins / Q000235:genetics; D020440:Gene Duplication; D020131:Genes, Duplicate / Q000235:genetics; D014644:Genetic Variation; D016681:Genome, Fungal / Q000235:genetics; D049751:Genome, Helminth / Q000235:genetics; D015801:Helminth Proteins / Q000235:genetics; D007438:Introns / Q000235:genetics; D012269:Ribosomal Proteins / Q000235:genetics; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D013045:Species Specificity
chemical_list: D005656:Fungal Proteins; D015801:Helminth Proteins; D012269:Ribosomal Proteins