orthologen

Orthologen, or orthologs, are genes in different species that originated from a single gene in the most recent common ancestor of those species and diverged through speciation. They frequently retain the same or similar function across species, although some functional divergence can occur after speciation.

Orthologs are contrasted with paralogs, which arise by gene duplication within a genome. Paralogs can evolve new or specialized functions, while orthologs are typically expected to maintain conserved roles that reflect the species’ shared ancestry. Identifying orthologous relationships is central to comparative genomics and functional annotation across species.

Detecting orthologs combines sequence similarity, phylogenetic analyses, and genomic context. Common methods include reciprocal best hits, where two genes are each other’s best match in different genomes, and tree-based approaches that map gene trees onto species trees. Clustering algorithms such as OrthoMCL, OrthoDB, eggNOG, InParanoid, and OMA are widely used to group orthologs and related paralogs. Synteny or conserved gene order can support orthology in closely related species.

Applications of orthology include transferring functional annotations between species, inferring ancestral gene repertoires, and studying conserved biological pathways. Orthology relationships underpin many studies in model organism research, evolutionary biology, and the reconstruction of evolutionary histories. Challenges include gene duplications, losses, incomplete lineage sorting, and horizontal gene transfer, which can complicate the inference of true orthologs and require careful, often tree-based, analysis.