Orphan gene

Orphan genes, ORFans, or taxonomically restricted genes are genes that lack a detectable homologue outside of a given species or lineage. Most genes have known homologues. Two genes are homologous when they share an evolutionary history, and the study of groups of homologous genes allows for an understanding of their evolutionary history and divergence. Common mechanisms that have been uncovered as sources for new genes through studies of homologues include gene duplication, exon shuffling, gene fusion and fission, etc. Studying the origins of a gene becomes more difficult when there is no evident homologue. The discovery that about 10% or more of the genes of the average microbial species is constituted by orphan genes raises questions about the evolutionary origins of different species as well as how to study and uncover the evolutionary origins of orphan genes.

In some cases, a gene can be classified as an orphan gene due to undersampling of the existing genome space. While it is possible that homologues exist for a given gene, that gene will still be classified as an orphan if the organisms harbouring homologues have not yet been discovered and had their genomes sequenced and properly annotated. For example, one study of orphan genes across 119 archaeal and bacterial genomes could identify that at least 56% were recently acquired from integrative elements (or mobile genetic elements) from non-cellular sources such as viruses and plasmids that remain to be explored and characterized, and another 7% arise through horizontal gene transfer from distant cellular sources (with an unknown proportion of the remaining 37% potentially coming from still unknown families of integrative elements). In other cases, limitations in computational methods for detecting homologues may result in missed homologous sequences and thus classification of a gene as an orphan.