MBE Advance Access published online on December 8, 2008
Molecular Biology and Evolution, doi:10.1093/molbev/msn281
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Research Article |
Origin of primate orphan genes: a comparative genomics approach
1 Evolutionary Genomics Group, Biomedical Informatics Research Programme, Fundació Institut Municipal d'Investigació Mèdica (FIMIM), Barcelona, Spain
2 Universitat Pompeu Fabra (UPF), Barcelona, Spain
3 Genes and Disease Program, Centre for Genomic Regulation (CRG-UPF) and CIBERESP, Barcelona, Catalonia, Spain
4 Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
Corresponding author contact information: M.Mar Albà, ICREA Research Professor, Biomedical Informatics Research Programme (GRIB), Fundació Institut Municipal d'Investigació Mèdica (FIMIM), Barcelona Biomedical Research Park (PRBB), Barcelona 08003, Spain, Phone: +34933160516, FAX: +34933160550, email: malba{at}imim.es
Received for publication October 22, 2008. Revision received November 26, 2008. Accepted for publication December 3, 2008.
Genomes contain a large number of genes that do not have recognisable homologues in other species, and which 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 and are mostly located in primate-specific genomic regions. This indicates frequent recruitment of transposable elements 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 non-coding genomic regions.
Key Words: Primate-specific gene • orphan gene • novel gene formation
* To whom correspondence should be addressed
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  C. Rancurel, M. Khosravi, A. K. Dunker, P. R. Romero, and D. Karlin Overlapping Genes Produce Proteins with Unusual Sequence Properties and Offer Insight into De Novo Protein Creation J. Virol., October 15, 2009; 83(20): 10719 - 10736. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Siepel Darwinian alchemy: Human genes from noncoding DNA Genome Res., October 1, 2009; 19(10): 1693 - 1695. [Full Text] [PDF]
|
|
|
|
|
|
D. G. Knowles and A. McLysaght Recent de novo origin of human protein-coding genes Genome Res., October 1, 2009; 19(10): 1752 - 1759. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 Correction for Tay et al., Global discovery of primate-specific genes in the human genome PNAS, August 18, 2009; 106(33): 14180 - 14180. [Full Text] [PDF]
|
|
|
|
 |
|
 J. J. Cai, E. Borenstein, R. Chen, and D. A. Petrov Similarly Strong Purifying Selection Acts on Human Disease Genes of All Evolutionary Ages Gen Biol Evol, June 22, 2009; 2009(0): 131 - 144. [Abstract] [Full Text] [PDF]
|
|