Genes from scratch--the evolutionary fate of de novo genes

Abstract

Although considered an extremely unlikely event, many genes emerge from previously noncoding genomic regions. This review covers the entire life cycle of such de novo genes. Two competing hypotheses about the process of de novo gene birth are discussed as well as the high death rate of de novo genes. Despite the high death rate, some de novo genes are retained and remain functional, even in distantly related species, through their integration into gene networks. Further studies combining gene expression with ribosome profiling in multiple populations across different species will be instrumental for an improved understanding of the evolutionary processes operating on de novo genes.

Keywords: de novo genes; orphans; population genetics; transcription.

Figure 1

Two competing models of de novo gene birth. Open reading frames (ORFs) are shown as colored blocks. Active transcription is symbolized by an arrow and the presence of translation by a peptide. Non-neutral phases are indicated by a broken box. (A) and (B) illustrate two versions of the expression first model. (A) The protogene model assumes that several short peptides are expressed and during the course of evolution they are combined into a larger de novo gene. (B) the ORF contains premature stop codons (yellow circles), which prevent the translation of the expressed mRNA; only after new mutations generate a full-length ORF is the functional de novo gene obtained. (C) The ORF first model states that a fully functional ORF is present but not expressed because the necessary regulatory signals are missing. Once new mutations generate functional transcription factor (TF) binding sites, the de novo gene is expressed and translated.

Figure 2

Phylogenetic analysis of de novo genes: de novo genes are identified in one focal species and their age is determined by the presence of an ortholog in sister taxa (red line). Using the parsimony criterion, the origin of the de novo gene is set to the most recent common ancestor of the focal species and the most diverged sister species. The evolutionary stability of de novo genes can be studied in those lineages that diverged after the origin of the de novo gene (green lines).