Ancestral gene synteny reconstruction improves extant species scaffolding

BMC Genomics

Research

Cedric Chauve¹  Vincent Berry²  Annie Chateau²  Sèverine Bérard³  Yoann Anselmetti⁴  Eric Tannier⁵ 

[1] Department of Mathematics, Simon Fraser University, 8888 University Drive, V5A 1S6, Burnaby, Canada;Institut de Biologie Computationnelle (IBC), Laboratoire d'Informatique, de Robotique et de Microélectronique de Montpellier (LIRMM), Université Montpellier - CNRS, 161 rue Ada, 34090, Montpellier, France;Institut des Sciences de l'Évolution de Montpellier (ISE-M), Place Eugène Bataillon, 34095, Montpellier, France;Institut de Biologie Computationnelle (IBC), Laboratoire d'Informatique, de Robotique et de Microélectronique de Montpellier (LIRMM), Université Montpellier - CNRS, 161 rue Ada, 34090, Montpellier, France;Institut des Sciences de l'Évolution de Montpellier (ISE-M), Place Eugène Bataillon, 34095, Montpellier, France;Laboratoire de Biométrie et Biologie Évolutive, LBBE, UMR CNRS 5558, University of Lyon 1, 43 boulevard du 11 novembre 1918, 69622, Villeurbanne, France;Laboratoire de Biométrie et Biologie Évolutive, LBBE, UMR CNRS 5558, University of Lyon 1, 43 boulevard du 11 novembre 1918, 69622, Villeurbanne, France;Institut National de Recherche en Informatique et en Automatique (INRIA) Grenoble Rhône-Alpes, 655 avenue de l'Europe, 38330, Montbonnot, France;

关键词: ancestral genome reconstruction;    genome scaffolding;    parsimony;    gene duplication/loss;    gene tree/species tree reconciliation;   

DOI  :  10.1186/1471-2164-16-S10-S11

来源: Springer

【 摘 要 】

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.

【 授权许可】

Unknown   
© Anselmetti et al.; 2015. This article is published under license to BioMed Central Ltd. 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.