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This article is part of the supplement: Proceedings of the Tenth Annual Research in Computational Molecular Biology (RECOMB) Satellite Workshop on Comparative Genomics

Open Access Proceedings

A consolidation algorithm for genomes fractionated after higher order polyploidization

Katharina Jahn, Chunfang Zheng, Jakub Kováč and David Sankoff*

Author Affiliations

Department of Mathematics and Statistics, University of Ottawa, 585 King Edward Avenue, Ottawa, Canada K1N 6N5

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BMC Bioinformatics 2012, 13(Suppl 19):S8  doi:10.1186/1471-2105-13-S19-S8

Published: 19 December 2012

Abstract

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.