ArticleBioinformatics (Oxford, England)2012
Evolution of gene neighborhoods within reconciled phylogenies.
Article in Bioinformatics (Oxford, England), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies.BMC biology · 2020Article
- Evolution through segmental duplications and losses: a Super-Reconciliation approach.Algorithms for molecular biology : AMB · 2020Article
- Phylogenetic signal from rearrangements in 18 Anopheles species by joint scaffolding extant and ancestral genomes.BMC genomics · 2018Article
- DeCoSTAR: Reconstructing the Ancestral Organization of Genes or Genomes Using Reconciled Phylogenies.Genome biology and evolution · 2017Article
- Efficient Gene Tree Correction Guided by Genome Evolution.PloS one · 2016Article
- Evolution of genes neighborhood within reconciled phylogenies: an ensemble approach.BMC bioinformatics · 2015Article
- Event inference in multidomain families with phylogenetic reconciliation.BMC bioinformatics · 2015Article
- The inference of gene trees with species trees.Systematic biology · 2015Review
- Reconstruction of an ancestral Yersinia pestis genome and comparison with an ancient sequence.BMC genomics · 2015Article
- Ancestral gene synteny reconstruction improves extant species scaffolding.BMC genomics · 2015Article
- Probabilistic modeling of the evolution of gene synteny within reconciled phylogenies.BMC bioinformatics · 2015Article
- Reconciliation of gene and species trees.BioMed research international · 2014Article
- Gene tree correction guided by orthology.BMC bioinformatics · 2013Article
- Lateral gene transfer, rearrangement, reconciliation.BMC bioinformatics · 2013Article
- Linearization of ancestral multichromosomal genomes.BMC bioinformatics · 2012Article
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Authors and funding
6 authors.
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No grant is acknowledged in the PubMed record.
Abstract
motivationMost models of genome evolution integrating gene duplications, losses and chromosomal rearrangements are computationally intract able, even when comparing only two genomes. This prevents large-scale studies that consider different types of genome structural variations.
resultsWe define an 'adjacency phylogenetic tree' that describes the evolution of an adjacency, a neighborhood relation between two genes, by speciation, duplication or loss of one or both genes, and rearrangement. We describe an algorithm that, given a species tree and a set of gene trees where the leaves are connected by adjacencies, computes an adjacency forest that minimizes the number of gains and breakages of adjacencies (caused by rearrangements) and runs in polynomial time. We use this algorithm to reconstruct contiguous regions of mammalian and plant ancestral genomes in a few minutes for a dozen species and several thousand genes. We show that this method yields reduced conflict between ancestral adjacencies. We detect duplications involving several genes and compare the different modes of evolution between phyla and among lineages. AVAILABILITY: C++ implementation using BIO++ package, available upon request to Sèverine Bérard. CONTACT: Severine.Berard@cirad.fr or Eric.Tannier@inria.fr SUPPLEMENTARY INFORMATION: Supplementary material is available at Bioinformatics online.
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