ArticleBMC bioinformatics2013
Lateral gene transfer, rearrangement, reconciliation.
Article in BMC bioinformatics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed, 26 citations in OpenAlex.
- Identification, evolution, and expression of GDSL-type Esterase/Lipase (GELP) gene family in three cotton species: a bioinformatic analysis.BMC genomics · 2023Article
- The Molecular Determinants of Thermoadaptation: Methanococcales as a Case Study.Molecular biology and evolution · 2021Article
- Genome size evolution in the Archaea.Emerging topics in life sciences · 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
- The inference of gene trees with species trees.Systematic biology · 2015Review
- Evolution of genes neighborhood within reconciled phylogenies: an ensemble approach.BMC bioinformatics · 2015Article
- Probabilistic modeling of the evolution of gene synteny within reconciled phylogenies.BMC bioinformatics · 2015Article
- Reconstruction of an ancestral Yersinia pestis genome and comparison with an ancient sequence.BMC genomics · 2015Article
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Authors and funding
4 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundModels of ancestral gene order reconstruction have progressively integrated different evolutionary patterns and processes such as unequal gene content, gene duplications, and implicitly sequence evolution via reconciled gene trees. These models have so far ignored lateral gene transfer, even though in unicellular organisms it can have an important confounding effect, and can be a rich source of information on the function of genes through the detection of transfers of clusters of genes.
resultWe report an algorithm together with its implementation, DeCoLT, that reconstructs ancestral genome organization based on reconciled gene trees which summarize information on sequence evolution, gene origination, duplication, loss, and lateral transfer. DeCoLT optimizes in polynomial time on the number of rearrangements, computed as the number of gains and breakages of adjacencies between pairs of genes. We apply DeCoLT to 1099 gene families from 36 cyanobacteria genomes.
conclusionDeCoLT is able to reconstruct adjacencies in 35 ancestral bacterial genomes with a thousand gene families in a few hours, and detects clusters of co-transferred genes. DeCoLT may also be used with any relationship between genes instead of adjacencies, to reconstruct ancestral interactions, functions or complexes. AVAILABILITY: http://pbil.univ-lyon1.fr/software/DeCoLT/
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