Gene-interleaving patterns of synteny in the <it>Saccharomyces cerevisiae </it>genome: are they proof of an ancient genome duplication event?

<p>Abstract</p> <p>Background</p> <p>Recent comparative genomic studies claim local syntenic gene-interleaving relationships in <it>Ashbya gossypii </it>and <it>Kluyveromyces waltii </it>are compelling evidence for an ancient whole-genome duplication event in <it>Saccharomyces cerevisiae</it>. We here test, using Hannenhalli-Pevzner rearrangement algorithms that address the multiple genome rearrangement problem, whether syntenic patterns are proof of paleopolyploidization.</p> <p>Results</p> <p>We focus on (1) pairwise comparison of gene arrangement sequences in <it>A. gossypii </it>and <it>S. cerevisiae</it>, (2) reconstruction of gene arrangements ancestral to <it>A. gossypii</it>, <it>S. cerevisiae</it>, and <it>K. waltii</it>, (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 <it>A. gossypii</it>, <it>S. cerevisiae</it>, and <it>K. waltii</it>, 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 <it>S. cerevisiae </it>and <it>K. waltii </it>lineages, but in the lineage leading to <it>K. waltii</it>. This is clearly incompatible with an ancient genome duplication event in <it>S. cerevisiae</it>.</p> <p>Conclusion</p> <p>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.</p> <p>Reviewers</p> <p>This article was reviewed by Kenneth H. Wolfe (nominated by Nicolas Galtier), Austin L. Hughes (nominated by Eugene Koonin), Mikhail S. Gelfand, and Mark Gerstein.</p>