论文信息 - Polyploids, genome halving and phylogeny

Polyploids, genome halving and phylogeny

MOTIVATION Autopolyploidization and allopolyploidization events multiply the number of chromosomes and genomic content. Genome rearrangement phylogenetics requires that all genomes analyzed have the same set of orthologs, so that it is not possible to include diploid and polyploid genomes in the same phylogeny. RESULTS We propose a framework for solving this difficulty by integrating the rearrangement median and genome halving algorithms. Though the framework is general, some problems remain open. We implement a heuristic solution to the prototypical case of a tree with one tetraploid and two diploid genomes, and apply it to study the evolution of cereals and of yeast.

[1] David Sankoff,et al. The Reconstruction of Doubled Genomes , 2003, SIAM J. Comput..

[2] Jens Stoye,et al. A Unifying View of Genome Rearrangements , 2006, WABI.

[3] David Sankoff,et al. Genome Halving with an Outgroup , 2006, Evolutionary bioinformatics online.

[4] B. Birren,et al. Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae , 2004, Nature.

[5] K. H. Wolfe,et al. Molecular evidence for an ancient duplication of the entire yeast genome , 1997, Nature.

[6] P. Pevzner,et al. Genome-scale evolution: reconstructing gene orders in the ancestral species. , 2002, Genome research.

[7] P. Philippsen,et al. The Ashbya gossypii Genome as a Tool for Mapping the Ancient Saccharomyces cerevisiae Genome , 2004, Science.

[8] Wei Zhao,et al. Gramene: a bird's eye view of cereal genomes , 2005, Nucleic Acids Res..

[9] B. Gaut,et al. DNA sequence evidence for the segmental allotetraploid origin of maize. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[10] Rita Casadio,et al. Algorithms in Bioinformatics, 5th International Workshop, WABI 2005, Mallorca, Spain, October 3-6, 2005, Proceedings , 2005, WABI.