ArticlePLoS computational biology2008
A methodological framework for the reconstruction of contiguous regions of ancestral genomes and its application to mammalian genomes.
Article in PLoS computational biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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23 citing papers in PubMed, 143 citations in OpenAlex.
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- Chromosome-level genome assembly reveals adaptive evolution of the invasive Amazon sailfin catfish (Pterygoplichthys pardalis).Communications biology · 2025Article
- AGO, a Framework for the Reconstruction of Ancestral Syntenies and Gene Orders.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Reconstruction of hundreds of reference ancestral genomes across the eukaryotic kingdom.Nature ecology & evolution · 2023Article
- A Chromosome-level assembly of the Japanese eel genome, insights into gene duplication and chromosomal reorganization.GigaScience · 2022Article
- Comparative mitogenomics elucidates the population genetic structure ofEvolutionary applications · 2022Article
- OMA orthology in 2021: website overhaul, conserved isoforms, ancestral gene order and more.Nucleic acids research · 2021Article
- Using in silico predicted ancestral genomes to improve the efficiency of paleogenome reconstruction.Ecology and evolution · 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
- Ancestral Genome Reconstruction on Whole Genome Level.Current genomics · 2017Review
- Reconstructing ancestral gene orders with duplications guided by synteny level genome reconstruction.BMC bioinformatics · 2016Article
- ProCARs: Progressive Reconstruction of Ancestral Gene Orders.BMC genomics · 2015Article
- Sampling and counting genome rearrangement scenarios.BMC bioinformatics · 2015Article
- Ancestral gene synteny reconstruction improves extant species scaffolding.BMC genomics · 2015Article
- PhylDiag: identifying complex synteny blocks that include tandem duplications using phylogenetic gene trees.BMC bioinformatics · 2014Article
- Evolution of gene neighborhoods within reconciled phylogenies.Bioinformatics (Oxford, England) · 2012Article
- A flexible ancestral genome reconstruction method based on gapped adjacencies.BMC bioinformatics · 2012Article
- Linearization of ancestral multichromosomal genomes.BMC bioinformatics · 2012Article
- Mapping ancestral genomes with massive gene loss: a matrix sandwich problem.Bioinformatics (Oxford, England) · 2011Article
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Authors and funding
2 authors at 2 institutions in 2 countries.
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No grant is acknowledged in the PubMed record.
Abstract
The reconstruction of ancestral genome architectures and gene orders from homologies between extant species is a long-standing problem, considered by both cytogeneticists and bioinformaticians. A comparison of the two approaches was recently investigated and discussed in a series of papers, sometimes with diverging points of view regarding the performance of these two approaches. We describe a general methodological framework for reconstructing ancestral genome segments from conserved syntenies in extant genomes. We show that this problem, from a computational point of view, is naturally related to physical mapping of chromosomes and benefits from using combinatorial tools developed in this scope. We develop this framework into a new reconstruction method considering conserved gene clusters with similar gene content, mimicking principles used in most cytogenetic studies, although on a different kind of data. We implement and apply it to datasets of mammalian genomes. We perform intensive theoretical and experimental comparisons with other bioinformatics methods for ancestral genome segments reconstruction. We show that the method that we propose is stable and reliable: it gives convergent results using several kinds of data at different levels of resolution, and all predicted ancestral regions are well supported. The results come eventually very close to cytogenetics studies. It suggests that the comparison of methods for ancestral genome reconstruction should include the algorithmic aspects of the methods as well as the disciplinary differences in data acquisition.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.