Origin of primate orphan genes

A comparative genomics approach

MacArena Toll-Riera, Nina Bosch, Nicolás Bellora, Robert Castelo, Lluis Armengol, Xavier P. Estivill, M. Mar Albà

Research output: Contribution to journalArticle

121 Citations (Scopus)

Abstract

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.

Original languageEnglish
Pages (from-to)603-612
Number of pages10
JournalMolecular Biology and Evolution
Volume26
Issue number3
DOIs
Publication statusPublished - Mar 2009
Externally publishedYes

Fingerprint

orphan
Orphaned Children
Genomics
primate
Primates
genomics
gene
Genes
genes
DNA Transposable Elements
codons
transposons
Codon
protein
Molecular Sequence Annotation
proteins
Organ Specificity
peptide
Proteins
peptides

Keywords

  • Novel gene formation
  • Orphan gene
  • Primate-specific gene

ASJC Scopus subject areas

  • Medicine(all)
  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics

Cite this

Toll-Riera, M., Bosch, N., Bellora, N., Castelo, R., Armengol, L., Estivill, X. P., & Mar Albà, M. (2009). Origin of primate orphan genes: A comparative genomics approach. Molecular Biology and Evolution, 26(3), 603-612. https://doi.org/10.1093/molbev/msn281

Origin of primate orphan genes : A comparative genomics approach. / Toll-Riera, MacArena; Bosch, Nina; Bellora, Nicolás; Castelo, Robert; Armengol, Lluis; Estivill, Xavier P.; Mar Albà, M.

In: Molecular Biology and Evolution, Vol. 26, No. 3, 03.2009, p. 603-612.

Research output: Contribution to journalArticle

Toll-Riera, M, Bosch, N, Bellora, N, Castelo, R, Armengol, L, Estivill, XP & Mar Albà, M 2009, 'Origin of primate orphan genes: A comparative genomics approach', Molecular Biology and Evolution, vol. 26, no. 3, pp. 603-612. https://doi.org/10.1093/molbev/msn281
Toll-Riera, MacArena ; Bosch, Nina ; Bellora, Nicolás ; Castelo, Robert ; Armengol, Lluis ; Estivill, Xavier P. ; Mar Albà, M. / Origin of primate orphan genes : A comparative genomics approach. In: Molecular Biology and Evolution. 2009 ; Vol. 26, No. 3. pp. 603-612.
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