Jul 23, 2015

Ancestral gene synteny reconstruction improves extant species scaffolding

BioRxiv : the Preprint Server for Biology
Yoann AnselmettiSeverine Berard

Abstract

We exploit the methodological similarity between ancestral genome reconstruction and extant genome scaffolding. We present a method, called \decopp\ 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 \decopp\ by s...Continue Reading

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Mentioned in this Paper

Abnormal Fragmented Structure
Genome
Genes
Reconstructive Surgical Procedures
Anatomical Space Structure
Gene Delivery Systems
Eutheria
Simulation
Gene Duplication Abnormality
Species

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