ArticleBMC bioinformatics2012
A flexible ancestral genome reconstruction method based on gapped adjacencies.
Article in BMC bioinformatics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed.
- From comparative gene content and gene order to ancestral contigs, chromosomes and karyotypes.Scientific reports · 2023Article
- IAGS: Inferring Ancestor Genome Structure under a Wide Range of Evolutionary Scenarios.Molecular biology and evolution · 2022Article
- On the reconstruction of the ancestral bacterial genomes in genus Mycobacterium and Brucella.BMC systems biology · 2018Article
- Reconstructing Yeasts Phylogenies and Ancestors from Whole Genome Data.Scientific reports · 2017Article
- Ancestral Genome Reconstruction on Whole Genome Level.Current genomics · 2017Review
- Genomes as documents of evolutionary history: a probabilistic macrosynteny model for the reconstruction of ancestral genomes.Bioinformatics (Oxford, England) · 2017Article
- Comparative genomics meets topology: a novel view on genome median and halving problems.BMC bioinformatics · 2016Article
- Fast ancestral gene order reconstruction of genomes with unequal gene content.BMC bioinformatics · 2016Article
- Reconstruction of ancestral chromosome architecture and gene repertoire reveals principles of genome evolution in a model yeast genus.Genome research · 2016Article
- A novel method of consensus pan-chromosome assembly and large-scale comparative analysis reveal the highly flexible pan-genome of Acinetobacter baumannii.Genome biology · 2015Article
- Probabilistic modeling of the evolution of gene synteny within reconciled phylogenies.BMC bioinformatics · 2015Article
- Reconstruction of ancestral gene orders using intermediate genomes.BMC bioinformatics · 2015Article
- Evolution of genes neighborhood within reconciled phylogenies: an ensemble approach.BMC bioinformatics · 2015Article
- ProCARs: Progressive Reconstruction of Ancestral Gene Orders.BMC genomics · 2015Article
- MLGO: phylogeny reconstruction and ancestral inference from gene-order data.BMC bioinformatics · 2014Article
- Reconstruction of ancestral gene orders using probabilistic and gene encoding approaches.PloS one · 2014Article
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3 authors.
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Abstract
backgroundThe "small phylogeny" problem consists in inferring ancestral genomes associated with each internal node of a phylogenetic tree of a set of extant species. Existing methods can be grouped into two main categories: the distance-based methods aiming at minimizing a total branch length, and the synteny-based (or mapping) methods that first predict a collection of relations between ancestral markers in term of "synteny", and then assemble this collection into a set of Contiguous Ancestral Regions (CARs). The predicted CARs are likely to be more reliable as they are more directly deduced from observed conservations in extant species. However the challenge is to end up with a completely assembled genome.
resultsWe develop a new synteny-based method that is flexible enough to handle a model of evolution involving whole genome duplication events, in addition to rearrangements, gene insertions, and losses. Ancestral relationships between markers are defined in term of Gapped Adjacencies, i.e. pairs of markers separated by up to a given number of markers. It improves on a previous restricted to direct adjacencies, which revealed a high accuracy for adjacency prediction, but with the drawback of being overly conservative, i.e. of generating a large number of CARs. Applying our algorithm on various simulated data sets reveals good performance as we usually end up with a completely assembled genome, while keeping a low error rate. AVAILABILITY: All source code is available at http://www.iro.umontreal.ca/~mabrouk.
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