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Ancestral gene synteny reconstruction improves extant species scaffolding

We exploit the methodological similarity between ancestral genome reconstruction and extant genome scaffolding. We present a method, called ARt-DeCo that constructs neighborhood relationships between genes or contigs, in both ancestral and extant genomes, in a phylogenetic context. It is able to han...

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Autores principales: Anselmetti, Yoann, Berry, Vincent, Chauve, Cedric, Chateau, Annie, Tannier, Eric, Bérard, Sèverine
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4603332/
https://www.ncbi.nlm.nih.gov/pubmed/26450761
http://dx.doi.org/10.1186/1471-2164-16-S10-S11
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author Anselmetti, Yoann
Berry, Vincent
Chauve, Cedric
Chateau, Annie
Tannier, Eric
Bérard, Sèverine
author_facet Anselmetti, Yoann
Berry, Vincent
Chauve, Cedric
Chateau, Annie
Tannier, Eric
Bérard, Sèverine
author_sort Anselmetti, Yoann
collection PubMed
description We exploit the methodological similarity between ancestral genome reconstruction and extant genome scaffolding. We present a method, called ARt-DeCo that constructs neighborhood relationships between genes or contigs, in both ancestral and extant genomes, in a phylogenetic context. It is able to handle dozens of complete genomes, including genes with complex histories, by using gene phylogenies reconciled with a species tree, that is, annotated with speciation, duplication and loss events. Reconstructed ancestral or extant synteny comes with a support computed from an exhaustive exploration of the solution space. We compare our method with a previously published one that follows the same goal on a small number of genomes with universal unicopy genes. Then we test it on the whole Ensembl database, by proposing partial ancestral genome structures, as well as a more complete scaffolding for many partially assembled genomes on 69 eukaryote species. We carefully analyze a couple of extant adjacencies proposed by our method, and show that they are indeed real links in the extant genomes, that were missing in the current assembly. On a reduced data set of 39 eutherian mammals, we estimate the precision and sensitivity of ARt-DeCo by simulating a fragmentation in some well assembled genomes, and measure how many adjacencies are recovered. We find a very high precision, while the sensitivity depends on the quality of the data and on the proximity of closely related genomes.
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spelling pubmed-46033322015-10-14 Ancestral gene synteny reconstruction improves extant species scaffolding Anselmetti, Yoann Berry, Vincent Chauve, Cedric Chateau, Annie Tannier, Eric Bérard, Sèverine BMC Genomics Research We exploit the methodological similarity between ancestral genome reconstruction and extant genome scaffolding. We present a method, called ARt-DeCo that constructs neighborhood relationships between genes or contigs, in both ancestral and extant genomes, in a phylogenetic context. It is able to handle dozens of complete genomes, including genes with complex histories, by using gene phylogenies reconciled with a species tree, that is, annotated with speciation, duplication and loss events. Reconstructed ancestral or extant synteny comes with a support computed from an exhaustive exploration of the solution space. We compare our method with a previously published one that follows the same goal on a small number of genomes with universal unicopy genes. Then we test it on the whole Ensembl database, by proposing partial ancestral genome structures, as well as a more complete scaffolding for many partially assembled genomes on 69 eukaryote species. We carefully analyze a couple of extant adjacencies proposed by our method, and show that they are indeed real links in the extant genomes, that were missing in the current assembly. On a reduced data set of 39 eutherian mammals, we estimate the precision and sensitivity of ARt-DeCo by simulating a fragmentation in some well assembled genomes, and measure how many adjacencies are recovered. We find a very high precision, while the sensitivity depends on the quality of the data and on the proximity of closely related genomes. BioMed Central 2015-10-02 /pmc/articles/PMC4603332/ /pubmed/26450761 http://dx.doi.org/10.1186/1471-2164-16-S10-S11 Text en Copyright © 2015 Anselmetti et al.; http://creativecommons.org/licenses/by/4.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research
Anselmetti, Yoann
Berry, Vincent
Chauve, Cedric
Chateau, Annie
Tannier, Eric
Bérard, Sèverine
Ancestral gene synteny reconstruction improves extant species scaffolding
title Ancestral gene synteny reconstruction improves extant species scaffolding
title_full Ancestral gene synteny reconstruction improves extant species scaffolding
title_fullStr Ancestral gene synteny reconstruction improves extant species scaffolding
title_full_unstemmed Ancestral gene synteny reconstruction improves extant species scaffolding
title_short Ancestral gene synteny reconstruction improves extant species scaffolding
title_sort ancestral gene synteny reconstruction improves extant species scaffolding
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4603332/
https://www.ncbi.nlm.nih.gov/pubmed/26450761
http://dx.doi.org/10.1186/1471-2164-16-S10-S11
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