Mapping gene gains and losses among metazoan full genomes using an integrated phylogenetic framework

Comparative genomics suffers from the lack of integrative tools embedded into a phylogenetic framework. The recently-developed MANTiS relational database (www.mantisdb.org) integrates phylogeny-based orthology/paralogy assignments with functional and expression data into an explicit phylogenetic framework, allowing users to explore phylogeny-driven (focusing on any set of branches), gene-driven (focusing on any set of genes), function/process-driven, and expression-driven questions. Here, we show that such integrative methods provide much improved mapping of gene gains than popular databases of orthologs (InParanoid, OrthoMCL, RoundUp). Furthermore, using published examples pertaining to (i) gains of chicken specific genes, and (ii) gains of genes involved in neural crest development, we demonstrate that the MANTiS relational database allows to easily and accurately perform comparative genomic analyses that were very tedious in the past.