The recurrent cycle of whole genome duplication (WGD) followed by massive duplicate gene loss (fractionation) differentiates plant evolutionary history from that of most other phylogenetic domains, where WGD has occurred relatively rarely, even on an evolutionary time scale. We discuss the mechanism of WGD and its biological consequences. We survey the prevalence of WGD in the flowering plants. We outline some of the major kinds of combinatorial optimization problems arising in computational biology for analyzing WGD. Fractionation and its consequences are the subject of mathematical modeling questions and further combinatorial algorithms. A strong connection is made between WGD in phylogenetic context and the theory of gene trees and species trees. We illustrate the analysis of WGD with studies involving a large number of sequenced plant genomes, including grape, the crucifers and other rosids, the asterid tomato, the eudicot Nelumbo nucifera and pineapple, a monocot.
Keywords: Angiosperm; Brassica; Consolidation; Core eudicots; Fractionation; Gene trees; Genome aliquoting; Genome halving; Nelumbo; Phylogeny; Pineapple; Rearrangement; Tomato.