Ancestral gene synteny reconstruction improves extant species scaffolding

Yoann Anselmetti 1, 2 Vincent Berry 3, 4 Cedric Chauve 5 Annie Chateau 3 Eric Tannier 1, 6 Sèverine Bérard 2
3 MAB - Méthodes et Algorithmes pour la Bioinformatique
LIRMM - Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier
6 BEAGLE - Artificial Evolution and Computational Biology
LBBE - Laboratoire de Biométrie et Biologie Evolutive - UMR 5558, Inria Grenoble - Rhône-Alpes, LIRIS - Laboratoire d'InfoRmatique en Image et Systèmes d'information
Abstract : 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.
Liste complète des métadonnées

Cited literature [38 references]  Display  Hide  Download

https://hal.archives-ouvertes.fr/hal-01180303
Contributor : Anne Jaigu <>
Submitted on : Thursday, October 15, 2015 - 3:24:11 PM
Last modification on : Wednesday, April 3, 2019 - 1:03:31 AM
Document(s) archivé(s) le : Thursday, April 27, 2017 - 4:47:19 AM

File

1471-2164-16-S10-S11.pdf
Publication funded by an institution

Identifiers

Citation

Yoann Anselmetti, Vincent Berry, Cedric Chauve, Annie Chateau, Eric Tannier, et al.. Ancestral gene synteny reconstruction improves extant species scaffolding. BMC Genomics, BioMed Central, 2015, 16 (Suppl 10), pp.S11. ⟨10.1186/1471-2164-16-S10-S11⟩. ⟨hal-01180303v2⟩

Share

Metrics

Record views

1183

Files downloads

139