De novo gene birth

De novo gene birth is the process by which new genes evolve from non-coding DNA. De novo genes represent a subset of novel genes, and may be protein-coding or instead act as RNA genes. The processes that govern de novo gene birth are not well understood, although several models exist that describe possible mechanisms by which de novo gene birth may occur.

Ancient de novo gene birth events are difficult to detect. Most studies of de novo genes to date have thus focused on young genes, typically taxonomically restricted genes (TRGs) that are present in a single species or lineage, including so-called orphan genes, defined as genes that lack any identifiable homolog.

Not all orphan genes arise de novo, but rather through fairly well characterized mechanisms such as gene duplication (including retroposition) or horizontal gene transfer followed by sequence divergence, or by gene fission/fusion.

Although de novo gene birth was once viewed as a highly unlikely occurrence, thousands of examples have now been described, and some researchers speculate that de novo gene birth could play a major role in evolutionary innovation, morphological specification, and adaptation, probably promoted by their low level of pleiotropy.

Conversely, criticism of the methodology and interpretation used to identify de novo gene candidates has appeared in the literature, including arguments that some reported cases may reflect artefacts of homology detection and annotation rather than genuine novelty. Rapid evolutionary divergence, along with the multiple and parallel loss of orthologs in some lineages, can give the false appearance of the emergence of a novel gene from scratch. Recent syntheses highlight both rapid progress and ongoing debates in de novo gene research, including challenges in identification, functional validation, and links to microproteins and random-peptide experiments.