Orphan and de novo Genes in Fungi and Animals: Identification, Origins and Functions

Ercan Seçkin , Dominique Colinet, Edoardo Sarti, Etienne GJ Danchin

Genes that don't have identifiable homologs in other species have been an intriguing and interesting topic of research for many years. These so-called orphan genes were first studied in yeast and since then, they have been found in many other species. This has fostered a whole field of research aiming at tracing back their evolutionary origin and functional significance. Orphan genes represent an important part of protein-coding genes in many species. Their presence was initially mainly hypothesized to result from high divergence from a pre-existing gene, with duplications or horizontal gene transfer facilitating their accelerated evolution. More recently, their possible de novo emergence from non-genic regions has gained particular interest. Some orphan genes are predicted to be involved in fertility, while others are involved in specific developmental stages, in adaptation mechanisms such as freeze protection or even human disease. However, there is currently no unified resource or synthesis that brings together existing knowledge about how often prevalent orphan genes are across different species and what their roles might be. In this review, we focus on orphan genes in animals and fungi (i.e opisthokonts). We provide a detailed summary of what has been discovered over time in terms of their prevalence in genomes, their origins as well as their roles in different biological contexts.