The Lost and Found: Unraveling the Functions of Orphan Genes

Abstract

Orphan Genes (OGs) are a mysterious class of genes that have recently gained significant attention. Despite lacking a clear evolutionary history, they are found in nearly all living organisms, from bacteria to humans, and they play important roles in diverse biological processes. The discovery of OGs was first made through comparative genomics followed by the identification of unique genes across different species. OGs tend to be more prevalent in species with larger genomes, such as plants and animals, and their evolutionary origins remain unclear but potentially arise from gene duplication, horizontal gene transfer (HGT), or de novo origination. Although their precise function is not well understood, OGs have been implicated in crucial biological processes such as development, metabolism, and stress responses. To better understand their significance, researchers are using a variety of approaches, including transcriptomics, functional genomics, and molecular biology. This review offers a comprehensive overview of the current knowledge of OGs in all domains of life, highlighting the possible role of dark transcriptomics in their evolution. More research is needed to fully comprehend the role of OGs in biology and their impact on various biological processes.

Keywords: ORFans; Orphan Genes; dark transcriptomics; evolution; functional characterization; high-throughput; sequencing.

Figure 1

Schematics of Orphan Genes (OG) identification. Sequencing is used to acquire genomic or transcriptomic data of target species. The comprehensive analysis tool integrating the online dataset, phylogenic information, and algorithm yields the separation of OGs and non-Orphan Genes (non-OGs). The inferred OGs are further characterized via gene function study. ******** indicates detailed trait content.

Figure 2

Pipeline of Orphan Genes (OGs) characterization. The inferred OGs are modified to be inserted into gene expression constructs for subsequent use in heterologous hosts, such as yeast or in planta systems. After transformation and selection, stable transgenics can be utilized in a variety of investigations. The potential function can be inferred based on data analysis of the functional studies. This figure was created using BioRender (https://biorender.com/accessed on 28 May 2023).