pangene

Pangene is a term occasionally used in genomics to denote a gene within the pangenome of a species. The pangenome is the full complement of genes found across multiple strains or individuals, including a core genome shared by all members and an accessory genome variably present. A pangene can refer to a single gene component or gene family (ortholog group) tracked across strains in a pangenome dataset. The term emphasizes the gene-level unit within the larger pan-genomic framework, as opposed to the abstract concept of the entire pangenome.

In practice, researchers identify pangene by annotating genomes, clustering homologous genes into families, and constructing presence–absence matrices across genomes. Pangene–level analyses explore patterns of gene gain and loss, horizontal transfer, and the distribution of functions related to adaptation, virulence, or metabolic capabilities. The concept is most commonly used in microbial genomics where high strain diversity leads to large accessory genomes; it is less standard in eukaryotic genomics, where the term "pangenome" is more widely used.

Limitations: the term pangene is not universally standardized; some authors use it interchangeably with the term "gene" within a pangenome, while others reserve it for individual gene families or elements in a pangenome dataset. See also pangenome, core genome, accessory genome, ortholog, pan-genome analysis.