Biology subjects

Eric Tannier

Publications and source records attributed to Eric Tannier.

2 recordsLinked to original sources

bioRxiv2016

Resolution and reconciliation of non-binary gene trees with transfers, duplications and losses

MotivationGene trees reconstructed from sequence alignments contain poorly supported branches when the phylogenetic signal in the sequences is weak. When a species tree is available, the signal of gains and losses of genes can be used to correctly resolve the unsupported parts of the gene history. Unfortunately, finding the best (i.e. most parsimonious) resolution has been shown to be NP-hard if transfers are considered as possible gene scale events, in addition to gene originations, duplications and losses.\n\nResultsWe propose an exact, parameterized algorithm solving this problem in single-exponential time, where the parameter is the number of connected branches of the gene tree that show low support from the sequence alignment or, equivalently, the maximum number of children of any node of the gene tree once the low-support branches have been collapsed. We propose a way to choose among optimal solutions based on the available information. We show the usability of this principle on several simulated and biological data sets. The results show a comparable or better quality than several other tested methods having similar goals, but with a lower running time and a guarantee on the optimality of the solution.\n\nAvailabilityOur algorithm has been integrated into the ecceTERA phylogeny package, available at http://mbb.univ-montp2.fr/MBB/download_sources/16_ecceTERA and which can be run online at http://mbb.univ-montp2.fr/MBB/subsection/softExec.php?soft=eccetera.\n\nContactceline.scornavacca@umontpellier.fr

Bioinformatics↗

bioRxiv2015

Ancestral gene synteny reconstruction improves extant species scaffolding

We exploit the methodological similarity between ancestral genome reconstruction and extant genome scaffolding. We present a method, called ARO_SCPCAPTC_SCPCAP-DO_SCPCAPEC_SCPCAPCO_SCPCAPOC_SCPCAP 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 ARO_SCPCAPTC_SCPCAP-DO_SCPCAPEC_SCPCAPCO_SCPCAPOC_SCPCAP 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.

Bioinformatics↗