title: Gene-interleaving patterns of synteny in the Saccharomyces cerevisiae genome: are they proof of an ancient genome duplication event?
abstract: BACKGROUND
  Recent comparative genomic studies claim local syntenic gene-interleaving relationships in Ashbya gossypii and Kluyveromyces waltii are compelling evidence for an ancient whole-genome duplication event in Saccharomyces cerevisiae. We here test, using Hannenhalli-Pevzner rearrangement algorithms that address the multiple genome rearrangement problem, whether syntenic patterns are proof of paleopolyploidization.
  
  
  RESULTS
  We focus on (1) pairwise comparison of gene arrangement sequences in A. gossypii and S. cerevisiae, (2) reconstruction of gene arrangements ancestral to A. gossypii, S. cerevisiae, and K. waltii, (3) synteny patterns arising within and between lineages, and (4) expected gene orientation of duplicate gene sets. The existence of syntenic patterns between ancestral gene sets and A. gossypii, S. cerevisiae, and K. waltii, and other evidence, suggests that gene-interleaving relationships are the natural consequence of topological rearrangements in chromosomes and that a more gradual scenario of genome evolution involving segmental duplication and recombination constitutes a more parsimonious explanation. Furthermore, phylogenetic trees reconstructed under alternative hypotheses placed the putative whole-genome duplication event after the divergence of the S. cerevisiae and K. waltii lineages, but in the lineage leading to K. waltii. This is clearly incompatible with an ancient genome duplication event in S. cerevisiae.
  
  
  CONCLUSIONS
  Because the presence of syntenic patterns appears to be a condition that is necessary, but not sufficient, to support the existence of the whole-genome duplication event, our results prompt careful re-evaluation of paleopolyploidization in the yeast lineage and the evolutionary meaning of syntenic patterns.
authors: Department of Crop Sciences, University of Illinois at Urbana-Champaign, 1101 W Peabody Drive, Urbana, IL 61801, USA.
authors: Nicolas
authors: N
authors: Martin
authors: Elizabeth A
authors: EA
authors: Ruedi
authors: Richard
authors: R
authors: Leduc
authors: Feng-Jie
authors: FJ
authors: Sun
authors: Gustavo
authors: G
authors: Caetano-Anollés
mesh_terms: D015825:Chromosomes, Fungal; D020440:Gene Duplication; D023061:Gene Order; D016681:Genome, Fungal; D007716:Kluyveromyces / Q000235:genetics; D010802:Phylogeny; D012441:Saccharomyces cerevisiae / Q000145:classification / Q000235:genetics*; D026801:Synteny