Reconstructing the History of Syntenies Through Super-Reconciliation

Delabre, Mattéo; El-Mabrouk, Nadia; Huber, Katharina T.; Lafond, Manuel; Moulton, Vincent; Noutahi, Emmanuel; Castellanos, Miguel Sautié

doi:10.1007/978-3-030-00834-5_10

Cited by 4 publications

(3 citation statements)

References 31 publications

(24 reference statements)

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“…In [94,95], the DL-reconciliation of a gene tree has been generalized to the DLreconciliation of a "synteny tree" (defined bellow) accounting for segmental duplications and losses. In this study, a synteny X is an ordered sequence of genes belonging to a genome s(X).…”

Section: Evolution Through Segmental Duplications and Lossesmentioning

confidence: 99%

“…In the case of gene families likely containing multiple copies in the same synteny, a way of doing can be to keep a single copy in each synteny. This is actually required for the super-reconciliation model considered in [94,95], as tandem duplications are not allowed in this model. Formally, given a set of gene trees represented as MUL-trees, i.e., trees with potentially repeated leaf-labels, the problem is to prune them in an appropriate way, keeping a single copy of each label.…”

Section: Synteny Tree Reconstructionmentioning

confidence: 99%

“…In [94,95], this problem is handled by a two-step algorithm: First label the internal nodes of T as duplications or speciation following the LCA-mapping (Figure 5(3), left), and then infer an optimal scenario of losses in agreement with this event-labeled treẽ T (Figure 5(3), right). This two-steps method has been shown exact, i.e., leading to a super-reconciliation of minimum cost (DL-distance).…”

Section: Super-reconciliationmentioning

confidence: 99%

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Predicting the Evolution of Syntenies—An Algorithmic Review

El-Mabrouk

2021

Algorithms

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Syntenies are genomic segments of consecutive genes identified by a certain conservation in gene content and order. The notion of conservation may vary from one definition to another, the more constrained requiring identical gene contents and gene orders, while more relaxed definitions just require a certain similarity in gene content, and not necessarily in the same order. Regardless of the way they are identified, the goal is to characterize homologous genomic regions, i.e., regions deriving from a common ancestral region, reflecting a certain gene co-evolution that can enlighten important functional properties. In addition of being able to identify them, it is also necessary to infer the evolutionary history that has led from the ancestral segment to the extant ones. In this field, most algorithmic studies address the problem of inferring rearrangement scenarios explaining the disruption in gene order between segments with the same gene content, some of them extending the evolutionary model to gene insertion and deletion. However, syntenies also evolve through other events modifying their content in genes, such as duplications, losses or horizontal gene transfers, i.e., the movement of genes from one species to another. Although the reconciliation approach between a gene tree and a species tree addresses the problem of inferring such events for single-gene families, little effort has been dedicated to the generalization to segmental events and to syntenies. This paper reviews some of the main algorithmic methods for inferring ancestral syntenies and focus on those integrating both gene orders and gene trees.

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Section: Evolution Through Segmental Duplications and Lossesmentioning

confidence: 99%

Section: Synteny Tree Reconstructionmentioning

confidence: 99%

Section: Super-reconciliationmentioning

confidence: 99%

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