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A consolidation algorithm for genomes fractionated after higher order polyploidization.

Jahn K, Zheng C, Kováč J, Sankoff D - BMC Bioinformatics (2012)

Bottom Line: In this paper, we present a new consolidation algorithm that extends and improves previous work in several directions.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Mathematics and Statistics, University of Ottawa, 585 King Edward Avenue, Ottawa, Canada K1N 6N5. sankoff@uottawa.ca

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.

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Simulation Schema. Schema for simulation of divergence between an ancient polyploid and a sister diploid.
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Figure 2: Simulation Schema. Schema for simulation of divergence between an ancient polyploid and a sister diploid.

Mentions: To study the effect of fractionation on rearrangement distances in hexaploid genomes for different rates of gene deletion, we conducted a series of experiments on simulated data. Simulated genomes were generated based on the schema shown in Figure 2. An ancestral diploid with 9000 genes was generated and randomly distributed over 7 chromosomes, to simulate the ancestor of the core eudicots. The genome was triplicated in one lineage to generate the ancestral hexaploid, modeled after the grapevine. Genome evolution was simulated by random chromosomal inversions and reciprocal translocation in the proportions 20:1. Double deletion and single deletion of genes were applied in the proportion 5.5:1.


A consolidation algorithm for genomes fractionated after higher order polyploidization.

Jahn K, Zheng C, Kováč J, Sankoff D - BMC Bioinformatics (2012)

Simulation Schema. Schema for simulation of divergence between an ancient polyploid and a sister diploid.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3526428&req=5

Figure 2: Simulation Schema. Schema for simulation of divergence between an ancient polyploid and a sister diploid.
Mentions: To study the effect of fractionation on rearrangement distances in hexaploid genomes for different rates of gene deletion, we conducted a series of experiments on simulated data. Simulated genomes were generated based on the schema shown in Figure 2. An ancestral diploid with 9000 genes was generated and randomly distributed over 7 chromosomes, to simulate the ancestor of the core eudicots. The genome was triplicated in one lineage to generate the ancestral hexaploid, modeled after the grapevine. Genome evolution was simulated by random chromosomal inversions and reciprocal translocation in the proportions 20:1. Double deletion and single deletion of genes were applied in the proportion 5.5:1.

Bottom Line: In this paper, we present a new consolidation algorithm that extends and improves previous work in several directions.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Mathematics and Statistics, University of Ottawa, 585 King Edward Avenue, Ottawa, Canada K1N 6N5. sankoff@uottawa.ca

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.

Show MeSH
Related in: MedlinePlus