Ancestral gene synteny reconstruction improves extant species scaffolding. (December 2015)

• Record Type: Journal Article
• Authors: Anselmetti, Yoann; Berry, Vincent; Chauve, Cedric; Chateau, Annie; Tannier, Eric; Bérard, Sèverine
• Is Part Of: BMC genomics. Volume 16:Number 10(2015)
• Page Start: 1
• Page End: 13
• Publication Date: 2015-12
• Subjects: ancestral genome reconstruction -- genome scaffolding -- parsimony -- gene duplication/loss -- gene tree/species tree reconciliation; Genomes -- Periodicals; Gene mapping -- Periodicals; Genomics -- Periodicals; Base Sequence -- Periodicals; Chromosome Mapping -- Periodicals; Genetic Techniques -- Periodicals; Sequence Analysis, DNA -- Periodicals; 572.8605
• DOI: 10.1186/1471-2164-16-S10-S11
• Languages: English
• ISSNs: 1471-2164

Abstract

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.