PT  - JOURNAL ARTICLE
AU  - Yoann Anselmetti
AU  - Vincent Berry
AU  - Cedric Chauve
AU  - Annie Chateau
AU  - Eric Tannier
AU  - Sèverine Bérard
TI  - Ancestral gene synteny reconstruction improves extant species scaffolding
AID  - 10.1101/023085
DP  - 2015 Jan 01
TA  - bioRxiv
PG  - 023085
4099  - http://biorxiv.org/content/early/2015/07/23/023085.short
4100  - http://biorxiv.org/content/early/2015/07/23/023085.full
AB  - 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.