Evolutionary Origin of Orphan Genes

Abstract

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.

Symbiont type and environmental factors affect transcriptome‐wide gene expression in the coral Montipora capitata

“…In the present study, we were only able to annotate a quarter of all transcribed host genes with Swiss‐Prot homologs, and to identify Pfam domains (on which GO annotations were based) in three‐quarters. Sequence homology may not be a reliable predictor of functional homology across greater phylogenetic distances, and genes that cannot be annotated may represent taxonomically restricted or highly divergent genes with important functional roles (Tautz & Domazet‐Lošo, ; Wissler, Gadau, Simola, Helmkampf, & Bornberg‐Bauer, ). These concerns appeared to be particularly pronounced in the site‐dependent DEGs.…”

The Discovery of De Novo Gene Evolution

“…This was initially considered an oddity, but it paved the way of how to study the question of de novo evolution-namely, by doing systematic genomic and transcriptional comparisons among multiple closely related lineages (Tautz, Neme, and Domazet-Lošo 2013). Toll-Riera et al (2009) conducted the first comparative analysis that allowed all possible models of gene evolution, including de novo evolution.…”

“…It is generally clear that proteins do not have to be folded to be functional (Dyson and Wright 2005), but it will also be important to revisit the question of whether folds can evolve convergently. Second, there is a continuum in gene emergence from neutrally expressed transcripts to non-coding but functional RNA transcripts to protein coding genes (Carvunis et al 2012;Tautz, Neme, and Domazet-Lošo 2013). In addition, even very short reading frames have been shown to be functional in some cases (Tautz 2009).…”

Importance of Genetic Studies in Consanguineous Populations for the Characterization of Novel Human Gene Functions

“…However, where not backed up by human observational studies, animal knockouts can be misleading as the underlying mechanism may be different in the model organism or the gene may have a different (or other acquired) function(s). In addition, some human genes lack homologues in the commonly analysed model organisms; some, termed “orphan” genes, may even have no homologues at all (Miklos et al., ) which is another limitation of these gene knockout studies (Tautz & Domazet‐Loso, ). Therefore, candidate genes derived from model organism “knockouts” cannot be directly translated to a human model until the same phenotype is also observed in humans.…”