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MBE Advance Access originally published online on December 8, 2008
Molecular Biology and Evolution 2009 26(3):603-612; doi:10.1093/molbev/msn281
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© The Author 2008. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org

Research Articles

Origin of Primate Orphan Genes: A Comparative Genomics Approach

Macarena Toll-Riera*,{dagger}, Nina Bosch{ddagger}, Nicolás Bellora*, Robert Castelo{dagger}, Lluis Armengol{ddagger}, Xavier Estivill{dagger},{ddagger} and M. Mar Albà*,{dagger},§

* Evolutionary Genomics Group, Biomedical Informatics Research Programme, Fundació Institut Municipal d'Investigació Mèdica, Barcelona, Spain
{dagger} Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
{ddagger} Genes and Disease Program, Centre for Genomic Regulation (CRG-UPF) and CIBERESP, Barcelona, Catalonia, Spain
§ Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain

E-mail: malba{at}imim.es.

Accepted for publication December 3, 2008.

Genomes contain a large number of genes that do not have recognizable homologues in other species and that are likely to be involved in important species-specific adaptive processes. The origin of many such "orphan" genes remains unknown. Here we present the first systematic study of the characteristics and mechanisms of formation of primate-specific orphan genes. We determine that codon usage values for most orphan genes fall within the bulk of the codon usage distribution of bona fide human proteins, supporting their current protein-coding annotation. We also show that primate orphan genes display distinctive features in relation to genes of wider phylogenetic distribution: higher tissue specificity, more rapid evolution, and shorter peptide size. We estimate that around 24% are highly divergent members of mammalian protein families. Interestingly, around 53% of the orphan genes contain sequences derived from transposable elements (TEs) and are mostly located in primate-specific genomic regions. This indicates frequent recruitment of TEs as part of novel genes. Finally, we also obtain evidence that a small fraction of primate orphan genes, around 5.5%, might have originated de novo from mammalian noncoding genomic regions.

Key Words: primate-specific gene • orphan gene • novel gene formation

Diethard Tautz, Associate Editor


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