Ancestral Gene Synteny Reconstruction Improves Extant Species Scaffolding

Resource type
Date created
2015
Authors/Contributors
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.
Document
Published as
Anselmetti Y, Berry V, Chauve C, Chateau A, Tannier E, Bérard S. Ancestral gene synteny reconstruction improves extant species scaffolding. BMC Genomics. 2015;16 Suppl 10:S11. doi: 10.1186/1471-2164-16-S10-S11. Epub 2015 Oct 2.
Publication title
BMC Genomics
Document title
Ancestral Gene Synteny Reconstruction Improves Extant Species Scaffolding
Date
2015
Volume
16
Publisher DOI
10.1186/1471-2164-16-S10-S11
Copyright statement
Copyright is held by the author(s).
Scholarly level
Peer reviewed?
Yes
Language
English
Member of collection
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1471-2164-16-S10-S11.pdf 2.07 MB

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