Colored de Bruijn Graphs and the Genome Halving Problem

Alekseyev, Max A.; Pevzner, Pavel A.

doi:10.1109/tcbb.2007.1002

Cited by 35 publications

(37 citation statements)

References 25 publications

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“…Our results have been reformulated recently by Alekseyev and Pevzner [1] using an alternative representation of the breakpoint graph. Subsequently, Sankoff and colleagues [16,15], and more recently Gavranović and Tannier [6], used variations of the genome halving strategy (Guided Genome Halving or GGH) to find the preduplicated ancestor of a doubled genome in the presence of a non-duplicated outgroup [16,15].…”

Section: Introductionmentioning

confidence: 84%

Reconstruction of Ancestral Genome Subject to Whole Genome Duplication, Speciation, Rearrangement and Loss

Bertrand

Gagnon

Blanchette

et al. 2010

Lecture Notes in Computer Science

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Abstract. Whole genome duplication (WGD) is a rare evolutionary event that has played a dramatic role in the diversification of most eucaryotic lineages. Given a set of species known to have evolved from a common ancestor through one or many rounds of WGD together with a set of genome rearrangements, and a phylogenetic tree for these species, the goal is to infer the pre-duplicated ancestral genomes. We use a two step approach: (1) Compute a score for each possible ancestral adjacency at each internal node of the phylogeny; (2) Combine adjacencies to form ancestral chromosomes. The main contribution of our method is the computation of a rigorous score for each potential ancestral adjacency (a, b), reflecting the maximum number of times a and b can be adjacent in the whole phylogeny, for any setting of ancestral genomes. We first apply our method on simulated datasets and show a high accuracy for adjacency prediction. We then infer the pre-duplicated ancestor of a set of 11 yeast species and compare it to a manually assembled ancestral genome obtained by Gordon et al. (2009).

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Section: Introductionmentioning

confidence: 84%

Reconstruction of Ancestral Genome Subject to Whole Genome Duplication, Speciation, Rearrangement and Loss

Bertrand

Gagnon

Blanchette

et al. 2010

Lecture Notes in Computer Science

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“…For reversal distance, these results have been reformulated [2] using an alternative representation of the breakpoint graph. There are also versions for DCJ [80,118] and for breakpoint distance [110].…”

Section: Genome Halvingmentioning

confidence: 99%

Analysis of Gene Order Evolution Beyond Single-Copy Genes

El-Mabrouk

Sankoff

2012

Methods in Molecular Biology

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The purpose of this chapter is to provide a comprehensive review of the field of genome rearrangement, i.e., comparative genomics based on representation of genomes as ordered sequences of signed genes. We specifically focus on the "hard part" of genome rearrangement, how to handle duplicated genes. The main questions are: how have present-day genomes evolved from a common ancestor? What are the most realistic evolutionary scenarios explaining the observed gene orders? What was the content and structure of ancestral genomes? We aim to provide a concise but complete overview of the field, starting with the practical problem of finding an appropriate representation of a genome as a sequence of ordered genes or blocks, namely the problems of orthology, paralogy and synteny block identification. We then consider three levels of gene organization: the gene family level (evolution by duplication, loss and speciation), the cluster level (evolution by tandem duplications) and the genome level (all types of rearrangement events, including whole genome duplication).

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“…In the case of genome halving, this simplification has been called the Weak Genome Halving Problem (Alekseyev and Pevzner, 2007a). We similarly define our simplified problem as follows: Notice that, in the case of a circular genome, a labelling of D maximizing the parameter C(G, D) also maximizes the DCJ formula, as C(G, D) = c(G, D) in this case.…”

Section: An Algorithm For the Double Distancementioning

confidence: 99%

“…When the ancestral genome D is unknown, the genome halving problem seeks for a perfectly duplicated genome D minimizing the rearrangement distance between G and D. In 2003, we have presented the first formal result related to genome duplication, which is an exact linear-time algorithm for solving the genome halving problem (El-Mabrouk and Sankoff, 2003). Our results have been reformulated by Alekseyev and Pevzner (Alekseyev and Pevzner, 2007a) using an alternative representation of the breakpoint graph. Subsequently, Sankoff and colleagues (Zheng et al, 2008b,a), and more recently Gavranović and Tannier (Gavranović and Tannier, 2010), used variations of the genome halving strategy (Guided Genome Halving or GGH) to find the preduplicated ancestor of a doubled genome in the presence of a non-duplicated outgroup (Zheng et al, 2008a,b).…”

Section: Introductionmentioning

confidence: 99%

Genome Halving and Double Distance with Losses

Savard

Gagnon

Bertrand

et al. 2011

Journal of Computational Biology

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Abstract. Given a phylogenetic tree involving Whole Genome Duplication events, we contribute to solving the problem of computing the rearrangement and DCJ distances on a branch of the tree linking a duplication node d to a speciation node or a leaf s. In the case of a genome G at s containing exactly two copies of each gene, the genome halving problem is to find a perfectly duplicated genome D at d minimizing the rearrangement distance with G. We generalize the existing exact linear-time algorithm for genome halving to the case of a genome G with missing gene copies. In the case of a known ancestral duplicated genome D, we develop a greedy approach for computing the distance between G and D, called the double distance. Two algorithms are developed in both cases of a genome G containing exactly two copies of each gene, or at most two copies of each gene (with missing gene copies). These algorithms are shown time-efficient and very accurate for both the rearrangement and DCJ distances.

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Colored de Bruijn Graphs and the Genome Halving Problem

Cited by 35 publications

References 25 publications

Reconstruction of Ancestral Genome Subject to Whole Genome Duplication, Speciation, Rearrangement and Loss

Reconstruction of Ancestral Genome Subject to Whole Genome Duplication, Speciation, Rearrangement and Loss

Analysis of Gene Order Evolution Beyond Single-Copy Genes

Genome Halving and Double Distance with Losses

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