Evolutionary Origin of Orphan Genes


Orphan genes are genes that occur in specific evolutionary lineages without similarity to genes outside of these lineages and have, therefore, alternatively been named taxonomically restricted genes. They were so far considered to emerge through duplication–divergence processes, but it is now becoming clear that they can also arise de novo out of noncoding deoxyribonucleic acid (DNA). This latter process may even occur much more frequently than previously assumed. It appears that genomes harbour many transcripts in a transition stage from nonfunctional to functional genes, also known as protogenes, which are exposed to evolutionary testing and can become fixed when they turn out to be useful. Orphan genes may have played key roles in generating lineage‐specific adaptations and could be a continuous source of evolutionary novelties. Their existence suggests that functional ribonucleic acids (RNAs) and proteins can relatively easily arise out of random nucleotide sequences, although these processes still need to be experimentally explored.

Key Concepts:

  • Orphan genes, or taxonomically restricted genes, have arisen at all levels of the phylogenetic hierarchy.

  • All genes that cannot be traced to the first cellular ancestor are orphan genes in some lineages.

  • New genes may not only arise through gene duplication, but also through de novo evolution.

  • Spurious transcripts can give rise to protogenes, from which new functional genes evolve.

  • Emergence of new genes from protogenes is an active process in all extant genomes.

  • New genes may first act as noncoding RNAs before obtaining a functional reading frame.

  • Overprinting of existing reading frames with new reading frames is another possibility of de novo evolution of gene functions.

  • Orphan genes may contribute to lineage‐specific adaptations.

  • Orphan genes may carry information on the evolutionary past that can be harnessed by the phylostratigraphic approach.

  • There is a continuous birth–death dynamics of gene evolution.

Keywords: gene emergence; phylostratigraphy; noncoding RNA; lineage‐specific adaptations; overprinting

Figure 1.

Examples of phylostratigraphic analyses of the mouse genome. (a) Depiction of 20 phylostrata (PS) ranging from the cellular origin to the extant house mouse (Mus musculusdomesticus) across the whole phylogeny. Each node is represented by several fully sequenced genomes (or at least extensive EST data), representing the respective phylogenetic split. All annotated protein‐coding genes of the mouse were subjected to BLAST analysis to find the oldest homologue within this phylogeny. The bar graphs to the right depict the numbers of genes found at the respective levels. The procedure of finding the oldest homologue is necessarily somewhat dependent on the BLAST cutoff chosen (see discussion on this topic in Tautz and Domazet‐Lošo, ), but the general pattern would not change much at different cutoffs or with different search algorithms. (b) Same analysis as above, but including the time frame for the separation of the nodes and gene numbers scaled to the respective time intervals (note the nonlinear time scale to allow an optimal resolution of the nodes). This depiction allows to infer rates of emergence of genes and shows that the rate is highest in the youngest lineage leading to the extant species.

Figure 2.

A general depiction of the life cycle of genes (after Carvunis et al., ). This representation assumes that genes emerge regularly out of nongenic sequences via a protogene phase. Once established as functional genes, they can expand into gene families. Alternatively, gene copies can also be lost again and become nongenic sequences.

Figure 3.

Depiction of the inference scheme for de novo evolution out of nongenic DNA. This scheme depicts a phylogeny of six related species, of which only species 6 is the focal species, where the hypothesis of a de novo gene evolution is tested. To make a solid case, one should show that the corresponding DNA region is present in the related species and synthenic in these species (indicated here by the depiction of the flanking genes Abc and Xyz). The region should also still be alignable, that is, the species that are compared should be sufficiently close to each other to ensure that even neutrally diverging sequences have not yet acquired too many mutations. Finally, all outgroups should not have a sign of a gene in the respective position, possibly apart of the most closely related ones, which could have a protogene or an RNA gene in the position.

Figure 4.

Example for a well studied overprinted locus. Both genes are tumour suppressor genes, but p16INK4a is the older one. p19ARF (ARF, alternative reading frame) originated through a new exon that splices to the central exon of p16INK4a but is translated from a different frame. Both proteins were shown to be functional (Quelle et al., ). Boxes indicate exons, filled boxes indicate protein‐coding regions.



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Tautz, Diethard, Neme, Rafik, and Domazet‐Lošo, Tomislav(May 2013) Evolutionary Origin of Orphan Genes. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0024601]