title: Ancestral gene synteny reconstruction improves extant species scaffolding.
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.
authors.forename: Yoann
authors.initials: Y
authors.lastname: Anselmetti
authors.forename: Vincent
authors.initials: V
authors.lastname: Berry
authors.forename: Cedric
authors.initials: C
authors.lastname: Chauve
authors.forename: Annie
authors.initials: A
authors.lastname: Chateau
authors.forename: Eric
authors.initials: E
authors.lastname: Tannier
authors.forename: Sèverine
authors.initials: S
authors.lastname: Bérard
mesh_terms: D000465:Algorithms; D000818:Animals; D019143:Evolution, Molecular; D020440:Gene Duplication; D016678:Genome; D008322:Mammals / Q000235:genetics*; D010802:Phylogeny; D026801:Synteny / Q000235:genetics