A pan-genome is a representation of the combined genomic diversity within a specified group of organisms. Sequence-based representations can integrate multiple genome assemblies and retain alternative versions of genomic regions, including structural variants and sequences absent from an individual reference [1]. Phased assemblies can further preserve the separate chromosome copies contributed by each sampled individual [2]. Gene-based representations group corresponding sequences into gene families and record their distribution across the sampled genomes. Computational representations include collections of sequences and graphs encoding alternative sequence paths [3]. Core genes occur throughout the sampled collection, whereas variable genes occur in only some members. In plants, this variable component includes gene presence–absence differences among accessions. The sampled genomes and criteria for grouping sequences must accompany interpretation of the reported repertoire [4][5].
- core genome
- accessory genome
- presence–absence variation
- genomic diversity
References
- Wen-Wei Liao; Mobin Asri; Jana Ebler; Daniel Doerr; Marina Haukness; Glenn Hickey; Shuangjia Lu; Julian K. Lucas; Jean Monlong; Haley J. Abel; et al. A Draft Human Pangenome Reference. Nature 2023, 617, 312-324, 10.1038/s41586-023-05896-x.
- Ting Wang; Lucinda Antonacci-Fulton; Kerstin Howe; Heather A. Lawson; Julian K. Lucas; Adam M. Phillippy; Alice B. Popejoy; Mobin Asri; Caryn Carson; Mark J. P. Chaisson; et al. The Human Pangenome Project: a Global Resource to Map Genomic Diversity. Nature 2022, 604, 437-446, 10.1038/s41586-022-04601-8.
- Rachel M. Sherman; Steven L. Salzberg; Pan-genomics in the Human Genome Era. Nat. Rev. Genet. 2020, 21, 243-254, 10.1038/s41576-020-0210-7.
- Jordan M. Eizenga; Adam M. Novak; Jonas A. Sibbesen; Simon Heumos; Ali Ghaffaari; Glenn Hickey; Xian Chang; Josiah D. Seaman; Robin Rounthwaite; Jana Ebler; et al. Pangenome Graphs. Annu. Rev. Genom. Hum. Genet. 2020, 21, 139-162, 10.1146/annurev-genom-120219-080406.
- Philipp E. Bayer; Agnieszka A. Golicz; Armin Scheben; Jacqueline Batley; David Edwards; Plant Pan-genomes are the New Reference. Nat. Plants 2020, 6, 914-920, 10.1038/s41477-020-0733-0.