Figure 4. Pangenomics at different taxonomic levels.

Reference sequences can be assembled for the genomes of both wild and domesticated plants. Diversity panels employed in pangenome studies may span different taxonomic levels, from single species to the tree of life. The term ‘super-pangenome’ is a useful shorthand to refer to pangenomics beyond the species level. Analysis methods differ according to whether the observed genomic variants segregate in a population of interfertile individuals or represent fixed differences between reproductively isolated species. Broadly speaking, intraspecific diversity fuels genetic mapping and breeding, whereas super-pangenomes hold answers to taxonomic and evolutionary questions. At higher taxonomic levels, taxon sampling cannot but look beyond crops, as the species that farmers attend to are in a minority.