Evolution of the protein domain repertoire of eukaryotes reveals strong functional patterns
© Zmasek and Godzik; licensee BioMed Central Ltd. 2010
Published: 11 October 2010
Eukaryotes exhibit massive variation in their morphological complexity, ranging from protists to basal animals, such as Trichoplax adhaerens with only four different cell types, to mammals with ~ 210 different cell types . Yet, the number of protein coding genes in eukaryotic genomes remains remarkably constant. Here, we attempt to shed some light on this paradox by analyzing eukaryotic genome evolution with a protein function centric view.
Materials and methods
Complete sets of predicted proteins for 114 eukaryotic genomes were analyzed with HMMER3 for Pfam domains. Ancestral domain sets were reconstructed using Dollo parsimony. Over- represented gene ontology (GO) terms were determined with Ontologizer 2.0.
This article is published under license to BioMed Central Ltd.