Katharina Jahn, Chunfang Zheng, Jakub Kovac, David Sankoff. A consolidation algorithm for genomes fractionated after higher order polyploidization. BMC Bioinformatics, 13 Suppl 19:S8. 2012.

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BACKGROUND: It has recently been shown that fractionation, the random loss of
excess gene copies after a whole genome duplication event, is a major cause of
gene order disruption. When estimating evolutionary distances between genomes
based on chromosomal rearrangement, fractionation inevitably leads to significant
overestimation of classic rearrangement distances. This bias can be largely
avoided when genomes are preprocessed by \"consolidation\", a procedure that
identifies and accounts for regions of fractionation. RESULTS: In this paper, we 
present a new consolidation algorithm that extends and improves previous work in 
several directions. We extend the notion of the fractionation region to use
information provided by regions where this process is still ongoing. The new
algorithm can optionally work with this new definition of fractionation region
and is able to process not only tetraploids but also genomes that have undergone 
hexaploidization and polyploidization events of higher order. Finally, this
algorithm reduces the asymptotic time complexity of consolidation from quadratic 
to linear dependence on the genome size. The new algorithm is applied both to
plant genomes and to simulated data to study the effect of fractionation in
ancient hexaploids.