OrthoMam: A Database of Single-copy Nuclear Markers for Placental Mammal Phylogenomics

Molecular sequence data have become the standard in modern day phylogenetics. Genomic data now provide the opportunity to select new markers that are potentially relevant for further resolving branches of the mammalian phylogenetic tree at various taxonomic levels. The EnsEMBL database was used to determine a set of orthologous genes from 12 available complete mammalian genomes. As targets for possible amplification and sequencing in additional taxa, more than 3,000 exons of length > 400 bp have been selected. A bioinformatic pipeline has been developed to provide evolutionary descriptors for these candidate markers in order to assess their potential phylogenetic utility. The resulting OrthoMaM (Orthologous Mammalian Markers) database can be queried and alignments can be downloaded through a dedicated web interface. Our database centered on complete genome information now makes possible to select promising markers to a given phylogenetic question or a systematic framework by querying a number of evolutionary descriptors. We expect the OrthoMaM database to be useful for further resolving the phylogenetic tree of placental mammals and for better understanding the evolutionary dynamics of their genomes.

Reference: Ranwez V., Delsuc F., Ranwez S., Belkhir K., Tilak M.-K. & Douzery E.J.P. (2007). OrthoMam: a database of orthologous genomic markers for placental mammal phylogenetics. BMC Evolutionary Biology 7: 241.