Polyploids, genome halving and phylogeny.
BACKGROUND
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.
Sankoff
David
D
Department of Mathematics and Statistics, University of Ottawa, Ottawa K1N 6N5, Canada. sankoff@uottawa.ca
Zheng
Chunfang
C
Zhu
Qian
Q
D000465:Algorithms; D005075:Biological Evolution; D002874:Chromosome Mapping / Q000379:methods*; D019143:Evolution, Molecular; D015321:Gene Rearrangement / Q000235:genetics*; D014644:Genetic Variation / Q000235:genetics*; D010802:Phylogeny; D011110:Polymorphism, Genetic; D011123:Polyploidy; D017422:Sequence Analysis, DNA / Q000379:methods