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Evolution of gene neighborhoods within reconciled phylogenies

Sèverine Bérard, Coralie Gallien, Bastien Boussau, Gergely J. Szöllősi, Vincent Daubin, Eric Tannier
2012 Computer applications in the biosciences : CABIOS  
Results: We 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  ...  We detect duplications involving several genes and compare the different modes of evolution between phyla and among lineages.  ...  neighborhoods based on a model of evolution allowing gene duplications.  ... 
doi:10.1093/bioinformatics/bts374 pmid:22962456 pmcid:PMC3436801 fatcat:xcqjzszkp5cshbdgvsv5cu7mza

Evolution of genes neighborhood within reconciled phylogenies: an ensemble approach [article]

Cedric Chauve, Yann Ponty, Joao Paulo Peirera Zanetti
2015 bioRxiv   pre-print
., computes parsimonious evolutionary scenarios for gene adjacencies, from pairs of reconciled gene trees.  ...  Results: We apply our algorithms to a dataset of mammalian gene trees and adjacencies, and observe a significant reduction of the number of syntenic conflicts observed in the resulting ancestral gene adjacencies  ...  A reconciled gene tree is also a binary tree that describes the evolution of a set of genes, called a gene family, through the evolutionary mechanisms of speciation, gene duplication and gene loss, within  ... 
doi:10.1101/026310 fatcat:vhc5v2bzqjhy3jzvjrhsqrenjy

Evolution of genes neighborhood within reconciled phylogenies: an ensemble approach

Cedric Chauve, Yann Ponty, João Zanetti
2015 BMC Bioinformatics  
., computes parsimonious evolutionary scenarios for gene adjacencies, from pairs of reconciled gene trees.  ...  Results: We apply our algorithms to a dataset of mammalian gene trees and adjacencies, and observe a significant reduction of the number of syntenic conflicts observed in the resulting ancestral gene adjacencies  ...  They introduced the notion of adjacency forest, that models the evolution of gene adjacencies within a phylogeny, motivated by the reconstruction of the architecture of ancestral genomes, and described  ... 
doi:10.1186/1471-2105-16-s19-s6 pmid:26696141 pmcid:PMC4686788 fatcat:tivavlil7jbbzpaxxoclnqwvwa

Evolution of Genes Neighborhood within Reconciled Phylogenies: An Ensemble Approach [chapter]

Cedric Chauve, Yann Ponty, João Paulo Pereira Zanetti
2014 Lecture Notes in Computer Science  
., computes parsimonious evolutionary scenarios for gene adjacencies, from pairs of reconciled gene trees.  ...  Results: We apply our algorithms to a dataset of mammalian gene trees and adjacencies, and observe a significant reduction of the number of syntenic conflicts observed in the resulting ancestral gene adjacencies  ...  They introduced the notion of adjacency forest, that models the evolution of gene adjacencies within a phylogeny, motivated by the reconstruction of the architecture of ancestral genomes, and described  ... 
doi:10.1007/978-3-319-12418-6_7 fatcat:vhb2c3zcqbhylcsv6jb476nwem

Probabilistic modeling of the evolution of gene synteny within reconciled phylogenies

Magali Semeria, Eric Tannier, Laurent Guéguen
2015 BMC Bioinformatics  
It uses reconciled phylogenies, which integrate sequence and gene content evolution.  ...  Probabilistic models of gene order evolution usually have to assume constant gene content or adopt a presence/absence coding of gene neighborhoods which is blind to complex events modifying gene content  ...  This work was performed using the computing facilities of the Computing Center LBBE/PRABI. This article has been published as part of BMC Bioinformatics Volume 16 Supplement 14, 2015  ... 
doi:10.1186/1471-2105-16-s14-s5 pmid:26452018 pmcid:PMC4603630 fatcat:czhsgbbkwnc55aywrumwp5wila

Assessing the robustness of parsimonious predictions for gene neighborhoods from reconciled phylogenies [article]

Ashok Rajaraman, Cedric Chauve, Yann Ponty (INRIA Saclay Ile de France, LIX)
2015 arXiv   pre-print
The availability of a large number of assembled genomes opens the way to study the evolution of syntenic character within a phylogenetic context.  ...  The DeCo algorithm, recently introduced by Bérard et al. allows the computation of parsimonious evolutionary scenarios for gene adjacencies, from pairs of reconciled gene trees.  ...  the convex hull computations within DeClone.  ... 
arXiv:1503.05292v2 fatcat:ympjtt44rnbdxhennuqbjekcma

Assessing the Robustness of Parsimonious Predictions for Gene Neighborhoods from Reconciled Phylogenies: Supplementary Material [chapter]

Ashok Rajaraman, Cedric Chauve, Yann Ponty
2015 Lecture Notes in Computer Science  
The availability of many assembled genomes opens the way to study the evolution of syntenic character within a phylogenetic context.  ...  ., computes parsimonious evolutionary scenarios for gene adjacencies, from pairs of reconciled gene trees.  ...  the convex hull computations within DeClone.  ... 
doi:10.1007/978-3-319-19048-8_22 fatcat:qn2uhpyswvagdkrazir2fd4vhe

The quest for orthologs: finding the corresponding gene across genomes

Arnold Kuzniar, Roeland C.H.J. van Ham, Sándor Pongor, Jack A.M. Leunissen
2008 Trends in Genetics  
(b) A reconciled gene tree (midpoint rooted) of mannose-binding lectin genes (experimentally verified) from mouse, rat and human.  ...  (conserved gene neighborhoods) and functional (ontologies) origins.  ... 
doi:10.1016/j.tig.2008.08.009 pmid:18819722 fatcat:4w6qrixl7naw7aoqko73vruavq

Synteny-guided resolution of gene trees clarifies the functional impact of whole genome duplications

Elise Parey, Alexandra Louis, Cédric Cabau, Yann Guiguen, Hugues Roest Crollius, Camille Berthelot, Koichiro Tamura
2020 Molecular biology and evolution  
Here we present SCORPiOs, a novel method to reconstruct gene phylogenies in the context of a known WGD event.  ...  We show that these synteny-guided phylogenies are more congruent with the species tree, with sequence evolution and with expected expression conservation patterns than those produced by state-of-the-art  ...  Acknowledgments We thank Pierre Vincens for the coordination of computing resources and all members of the GenoFish consortium for fruitful discussions. This work is funded by ANR GenoFish (Grant No.  ... 
doi:10.1093/molbev/msaa149 pmid:32556216 fatcat:lfyiprkzdnbsxgouylkgnlxic4

Efficient error correction algorithms for gene tree reconciliation based on duplication, duplication and loss, and deep coalescence

Ruchi Chaudhary, J Gordon Burleigh, Oliver Eulenstein
2012 BMC Bioinformatics  
Gene tree -species tree reconciliation problems infer the patterns and processes of gene evolution within a species tree.  ...  These algorithms improve on the current solutions by a factor of n for searching SPR neighborhoods and n 2 for searching TBR neighborhoods, where n is the number of taxa in the given gene tree.  ...  This work was conducted in parts with support from the Gene Tree Reconciliation Working Group at NIMBioS through NSF award EF-0832858, with additional support from the University of Tennessee.  ... 
doi:10.1186/1471-2105-13-s10-s11 pmid:22759416 pmcid:PMC3382437 fatcat:wfrpopwrqzh25f4es4nlbyno6a

Repeated gain and loss of a single gene modulates the evolution of vascular plant pathogen lifestyles

Emile Gluck-Thaler, Aude Cerutti, Alvaro L. Perez-Quintero, Jules Butchacas, Verónica Roman-Reyna, Vishnu Narayanan Madhavan, Deepak Shantharaj, Marcus V. Merfa, Céline Pesce, Alain Jauneau, Taca Vancheva, Jillian M. Lang (+14 others)
2020 Science Advances  
Our results overall demonstrate how the gain and loss of single loci can facilitate the evolution of complex ecological traits.  ...  The contrasting features of vascular and nonvascular diseases suggest distinct etiologies, but the basis for each remains unclear.  ...  We built nucleotide-based ML phylogenies of cbsA and the genes from each neighborhood type and manually reconciled their evolutionary histories with the consensus species tree using a combination of parsimony-based  ... 
doi:10.1126/sciadv.abc4516 pmid:33188025 pmcid:PMC7673761 fatcat:kufzxglqu5f6bp2pnxzzzwr2me

Zombi: a phylogenetic simulator of trees, genomes and sequences that accounts for dead linages

2019 Bioinformatics  
Here we present Zombi, a tool to simulate the evolution of species, genomes and sequences in silico, that considers for the first time the evolution of genomes in extinct lineages.  ...  rates through time, simulating explicitly intergenic sequences of variable length and outputting gene tree-species tree reconciliations.  ...  Acknowledgements We thank Vincent Daubin, Wandrille Duchemin, Nicolas Lartillot and Thibault Latrille for insightful discussions during the preparation of this manuscript.  ... 
doi:10.1093/bioinformatics/btz710 pmid:31566657 pmcid:PMC7031779 fatcat:wfyywcllkreblankienj7tiama

The Distant Siblings—A Phylogenomic Roadmap Illuminates the Origins of Extant Diversity in Fungal Aromatic Polyketide Biosynthesis

Grzegorz Koczyk, Adam Dawidziuk, Delfina Popiel
2015 Genome Biology and Evolution  
Although the majority of discord between species and gene history is explained by ancient duplications, this landscape has been altered by more recent duplications, as well as multiple horizontal gene  ...  By reconciling the history of over 400 nonreducing polyketide synthases (NR-PKSs) with corresponding species history, we demonstrate that extant fungal NR-PKSs are clades of distant siblings, originating  ...  The authors thank Morgan Price for access to FastTreeMP version with LG matrix support and Nicholas Lartillot for helpful advice regarding tests of PhyloBayes-MPI results.  ... 
doi:10.1093/gbe/evv204 pmid:26537223 pmcid:PMC5635595 fatcat:5vqyvoeud5hqpnztnq5nnr236y

Repeated gain and loss of a single gene modulates the evolution of vascular pathogen lifestyles [article]

Emile Gluck-Thaler, Aude Cerutti, Alvaro Perez Quintero, Jules Butchacas, Veronica Roman-Reyna, Vishnu Narayanan Madhaven, Deepak Shantharaj, Marcus V Merfa, Celine Pesce, Alain Jauneau, Jillian M Lang, Caitilyn Allen (+15 others)
2020 bioRxiv   pre-print
Our results overall demonstrate how the gain and loss of single loci can facilitate the evolution of complex ecological traits.  ...  The contrasting features of vascular and non-vascular diseases suggest distinct etiologies, but the basis for each remains unclear.  ...  in cbsA's extant distribution. 435 436 We built nucleotide-based ML phylogenies of cbsA and the genes from each neighborhood type, 437 and manually reconciled their evolutionary histories with the consensus  ... 
doi:10.1101/2020.04.24.058529 fatcat:ppeybb4iy5dspma4p45m55l63m

Inferring Orthology and Paralogy [chapter]

Adrian M. Altenhoff, Christophe Dessimoz
2012 Msphere  
Finally, we review typical applications of orthologous genes, groups, and reconciled trees and conclude with thoughts on future methodological developments.  ...  We survey both graph-based approaches (and their various grouping strategies) and tree-based approaches, which solve the more general problem of gene/species tree reconciliation.  ...  Part of this chapter started as assignment for the graduate course "Reviews in Computational Biology" (263-5151-00L) at ETH Zurich.  ... 
doi:10.1007/978-1-61779-582-4_9 pmid:22407712 fatcat:52mxshbwvzffrllmaipbidh5ky
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