Yeast Ancestral Genome Reconstructions: The Possibilities of Computational Methods II

Chauve, Cédric; Gavranović, Haris; Ouangraoua, Aïda; Tannier, Éric

doi:10.1089/cmb.2010.0092

Cited by 25 publications

(26 citation statements)

References 33 publications

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“…Reconstructing the ancestral genomes [15, 25] as an ordering of synteny blocks defined through whole genome alignment of the extant genomes [26] can create a more contiguous genome structure. The length of such blocks can be controlled, and is typically defined to be greater than 100 kb.…”

Section: Introductionmentioning

confidence: 99%

Reconstructing ancestral gene orders with duplications guided by synteny level genome reconstruction

Rajaraman

2016

BMC Bioinformatics

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BackgroundReconstructing ancestral gene orders in the presence of duplications is important for a better understanding of genome evolution. Current methods for ancestral reconstruction are limited by either computational constraints or the availability of reliable gene trees, and often ignore duplications altogether. Recently, methods that consider duplications in ancestral reconstructions have been developed, but the quality of reconstruction, counted as the number of contiguous ancestral regions found, decreases rapidly with the number of duplicated genes, complicating the application of such approaches to mammalian genomes. However, such high fragmentation is not encountered when reconstructing mammalian genomes at the synteny-block level, although the relative positions of genes in such reconstruction cannot be recovered.ResultsWe propose a new heuristic method, MultiRes, to reconstruct ancestral gene orders with duplications guided by homologous synteny blocks for a set of related descendant genomes. The method uses a synteny-level reconstruction to break the gene-order problem into several subproblems, which are then combined in order to disambiguate duplicated genes. We applied this method to both simulated and real data. Our results showed that MultiRes outperforms other methods in terms of gene content, gene adjacency, and common interval recovery.ConclusionsThis work demonstrates that the inclusion of synteny-level information can help us obtain better gene-level reconstructions. Our algorithm provides a basic toolbox for reconstructing ancestral gene orders with duplications. The source code of MultiRes is available on https://github.com/ma-compbio/MultiRes.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-016-1262-8) contains supplementary material, which is available to authorized users.

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Section: Introductionmentioning

confidence: 99%

Reconstructing ancestral gene orders with duplications guided by synteny level genome reconstruction

Rajaraman

2016

BMC Bioinformatics

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“…On large datasets, especially with matrices with an arbitrary number of entries 1 per row, some connected components of the overlap graph can be very large (see the data in [8] for example). In order to speed up the computations, algorithmic design and engineering developments are required, both in the joint generation algorithm and in the problem of testing the C1P for matrices after rows are added or removed.…”

Section: Discussionmentioning

confidence: 99%

Minimal Conflicting Sets for the Consecutive Ones Property in Ancestral Genome Reconstruction

Chauve

Haus

Stephen

et al. 2009

Comparative Genomics

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Abstract. A binary matrix has the Consecutive Ones Property (C1P) if its columns can be ordered in such a way that all 1's on each row are consecutive. A Minimal Conflicting Set is a set of rows that does not have the C1P, but every proper subset has the C1P. Such submatrices have been considered in comparative genomics applications, but very little is known about their combinatorial structure and efficient algorithms to compute them. We first describe an algorithm that detects rows that belong to Minimal Conflicting Sets. This algorithm has a polynomial time complexity when the number of 1s in each row of the considered matrix is bounded by a constant. Next, we show that the problem of computing all Minimal Conflicting Sets can be reduced to the joint generation of all minimal true clauses and maximal false clauses for some monotone boolean function. We use these methods on simulated data related to ancestral genome reconstruction to show that computing Minimal Conflicting Set is useful in discriminating between true positive and false positive ancestral syntenies. We also study a dataset of yeast genomes and address the reliability of an ancestral genome proposal of the Saccahromycetaceae yeasts.Draft, do not distribute.

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“…These differences are a result of a succession of rearrangements from an ancestral architecture, called a rearrangement scenario. In the quest to infer accurate rearrangement scenarios, it is often the case that the parsimony principal alone does not impose enough constraints [3].…”

Section: Introductionmentioning

confidence: 99%

Rearrangement Scenarios Guided by Chromatin Structure

Pulicani

Simonaitis

Swenson³

2017

Preprint

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Abstract. Genome architecture can be drastically modified through a succession of large-scale rearrangements. In the quest to infer accurate ancestral rearrangement scenarios, it is often the case that parsimony principal alone does not impose enough constraints. Thus, the current challenge is to consider more biological information in the inference process. In previous work, we introduced a model for such a task, based on a partition into equivalence classes of the adjacencies between genes. Such a partition is amenable to the representation of spacial constraints as given by Hi-C data. A major open question is the validity of such a model. In this note, we show that the quality of a clustering of the adjacencies based on Hi-C data is directly correlated to the quality of a rearrangement scenario that we compute between Drosophila melanogaster and D. yakuba.

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Yeast Ancestral Genome Reconstructions: The Possibilities of Computational Methods II

Cited by 25 publications

References 33 publications

Reconstructing ancestral gene orders with duplications guided by synteny level genome reconstruction

Reconstructing ancestral gene orders with duplications guided by synteny level genome reconstruction

Minimal Conflicting Sets for the Consecutive Ones Property in Ancestral Genome Reconstruction

Rearrangement Scenarios Guided by Chromatin Structure

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