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A pan-genome represents the full complement of diversity within a clade, or the union of all genes or SNPs across a representative selection of genomes. One of the first pan-genomes was that of Streptococcus agalactiae, introduced in 2005. Since then, with the acceleration of whole-genome sequencing technology, pan-genomes have been generated across a wide range of multicellular eukaryotes. This presentation will outline the history of pan-genomes, the categories of pan-genomes, advances in pan-genome assessment, and the challenges of representing the diversity of a taxonomic clade in complex eukaryotes.