Pangenomics Comes of Age: From Bacteria to Plant and Animal Applications

The pangenome refers to a collection of genomic sequence found in the entire species or population rather than in a single individual; the sequence can be core, present in all individuals, or accessory (variable or dispensable), found in a subset of individuals only. While pangenomic studies were first undertaken in bacterial species, developments in genome sequencing and assembly approaches have allowed construction of pangenomes for eukaryotic organisms, fungi, plants, and animals, including two large-scale human pangenome projects. Analysis of the these pangenomes revealed key differences, most likely stemming from divergent evolutionary histories, but also surprising similarities. The pangenome is composed of core genes/sequences found in all individuals and accessory genes/sequences found in some individuals only.While introduced in prokaryotic research, the pangenome concept has been shown to be applicable across tree of life, including protists, fungi, plants, and animals.Studies of bacterial, fungal, plant, and animal pangenomes allowed identification of a large number of accessory genes/sequences that were missing from reference genomes. The accessory genes are often over-represented in functions related to signaling and virulence/defense response.Moving from using a single genome to a pangenome as a reference will improve variant calling and identification of genes associated with key traits.