Prediction of Contiguous Regions in the Amniote Ancestral Genome

Aïda Ouangraoua (1, 2, 3) , Frédéric Boyer (4) , Andrew Mcpherson (1) , Eric Tannier (5) , Cedric Chauve (1)

1 SFU - Department of Mathematics [Burnaby]
2 LaBRI - Laboratoire Bordelais de Recherche en Informatique
3 Pulmonology Department
4 Laboratoire Biologie, Informatique et Mathématiques
5 BPGE - Bioinformatique, phylogénie et génomique évolutive

We investigate the problem of inferring contiguous ancestral regions (CARs) of the genome of the last common ancestor of all extant amniotes, based on the currently sequenced and assembled amniote genomes as ingroups and three teleost fish genomes as outgroups. We combine a methodological framework using conserved syntenies computed from whole genome alignments of amniote species together with double conserved syntenies (DCS) using gene families from amniote and fish genomes, to take into account the whole genome duplication that occurred in the teleost lineage. From these comparisons, ancestral genome segments are computed using techniques inspired by physical mapping. Due to the difficulty caused by the whole genome duplication and the large evolutionary distance to the closest assembled outgroup, very few methods have been published with a reconstruction of the amniote ancestral genome. This one is the first which is founded on a simple and formal methodological framework, whose good stability is shown and whose CARs cover large regions of the human and chicken genomes.

Domaines: Bio-informatique [q-bio.QM]; Bio-Informatique, Biologie Systémique [q-bio.QM]

Aïda Ouangraoua, Frédéric Boyer, Andrew Mcpherson, Eric Tannier, Cedric Chauve. Prediction of Contiguous Regions in the Amniote Ancestral Genome. ISBRA 2009, 5th International Symposium on Bioinformatics Research and Applications,, May 2009, Fort Lauderdale, Florida, United States. ⟨10.1007/978-3-642-01551-9_18⟩. ⟨hal-00368187⟩