Orthogroups

An orthogroup is a collection of genes that are descended from a single gene in the last common ancestor of the species being considered. Orthogroups are a practical way to organize gene content across multiple genomes because they group together all descendants of that ancestral gene, including both orthologs (genes in different species that originated by speciation) and paralogs (genes related by duplication within a genome after speciation). An orthogroup may therefore contain multiple genes from the same species if gene duplication has occurred.

Orthogroups are defined with respect to a specified set of species, and their composition can change as more genomes are included. They are typically inferred from whole-proteome analyses using sequence similarity, phylogenetic reconciliation, or clustering methods. Common approaches include graph-based clustering and tree-based reconciliation. Tools such as OrthoFinder, OrthoMCL, OMA, and eggNOG are used to identify orthogroups from proteomes.

Applications of orthogroups include facilitating comparative genomics, transferring functional annotations across species, and reconstructing ancestral gene content. They provide a framework for analyzing gene family evolution—duplications, losses, and speciation events—and support phylogenomic studies and cross-species functional inference. By focusing on orthogroups, researchers can study how gene content has evolved across lineages and draw inferences about the functions of genes in less well-annotated genomes.