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Peng, Y. Pan-Genome. Encyclopedia. Available online: https://encyclopedia.pub/entry/61051 (accessed on 02 November 2026).
Peng Y. Pan-Genome. Encyclopedia. Available at: https://encyclopedia.pub/entry/61051. Accessed November 02, 2026.
Peng, Yu. "Pan-Genome" Encyclopedia, https://encyclopedia.pub/entry/61051 (accessed November 02, 2026).
Peng, Y. (2026, October 17). Pan-Genome. In Encyclopedia. https://encyclopedia.pub/entry/61051
Peng, Yu. "Pan-Genome." Encyclopedia. Web. 17 October, 2026.

Pan-Genome

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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
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References

  1. Wen-Wei Liao; Mobin Asri; Jana Ebler; Daniel Doerr; Marina Haukness; Glenn Hickey; Shuangjia Lu; Julian K. Lucas; Jean Monlong; Haley J. Abel; Silvia Buonaiuto; Xian H. Chang; Haoyu Cheng; Justin Chu; Vincenza Colonna; Jordan M. Eizenga; Xiaowen Feng; Christian Fischer; Robert S. Fulton; Shilpa Garg; Cristian Groza; Andrea Guarracino; William T. Harvey; Simon Heumos; Kerstin Howe; Miten Jain; Tsung-Yu Lu; Charles Markello; Fergal J. Martin; Matthew W. Mitchell; Katherine M. Munson; Moses Njagi Mwaniki; Adam M. Novak; Hugh E. Olsen; Trevor Pesout; David Porubsky; Pjotr Prins; Jonas A. Sibbesen; Jouni Sirén; Chad Tomlinson; Flavia Villani; Mitchell R. Vollger; Lucinda L. Antonacci-Fulton; Gunjan Baid; Carl A. Baker; Anastasiya Belyaeva; Konstantinos Billis; Andrew Carroll; Pi-Chuan Chang; Sarah Cody; Daniel E. Cook; Robert M. Cook-Deegan; Omar E. Cornejo; Mark Diekhans; Peter Ebert; Susan Fairley; Olivier Fedrigo; Adam L. Felsenfeld; Giulio Formenti; Adam Frankish; Yan Gao; Nanibaa’ A. Garrison; Carlos Garcia Giron; Richard E. Green; Leanne Haggerty; Kendra Hoekzema; Thibaut Hourlier; Hanlee P. Ji; Eimear E. Kenny; Barbara A. Koenig; Alexey Kolesnikov; Jan O. Korbel; Jennifer Kordosky; Sergey Koren; HoJoon Lee; Alexandra P. Lewis; Hugo Magalhães; Santiago Marco-Sola; Pierre Marijon; Ann McCartney; Jennifer McDaniel; Jacquelyn Mountcastle; Maria Nattestad; Sergey Nurk; Nathan D. Olson; Alice B. Popejoy; Daniela Puiu; Mikko Rautiainen; Allison A. Regier; Arang Rhie; Samuel Sacco; Ashley D. Sanders; Valerie A. Schneider; Baergen I. Schultz; Kishwar Shafin; Michael W. Smith; Heidi J. Sofia; Ahmad N. Abou Tayoun; Françoise Thibaud-Nissen; Francesca Floriana Tricomi; Justin Wagner; Brian Walenz; Jonathan M. D. Wood; Aleksey V. Zimin; Guillaume Bourque; Mark J. P. Chaisson; Paul Flicek; Adam M. Phillippy; Justin M. Zook; Evan E. Eichler; David Haussler; Ting Wang; Erich D. Jarvis; Karen H. Miga; Erik Garrison; Tobias Marschall; Ira M. Hall; Heng Li; Benedict Paten; A Draft Human Pangenome Reference. Nature 2023, 617, 312-324. [CrossRef]
  2. 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; Xian Chang; Robert Cook-Deegan; Adam L. Felsenfeld; Robert S. Fulton; Erik P. Garrison; Nanibaa’ A. Garrison; Tina A. Graves-Lindsay; Hanlee Ji; Eimear E. Kenny; Barbara A. Koenig; Daofeng Li; Tobias Marschall; Joshua F. McMichael; Adam M. Novak; Deepak Purushotham; Valerie A. Schneider; Baergen I. Schultz; Michael W. Smith; Heidi J. Sofia; Tsachy Weissman; Paul Flicek; Heng Li; Karen H. Miga; Benedict Paten; Erich D. Jarvis; Ira M. Hall; Evan E. Eichler; David Haussler; the Human Pangenome Reference Consortium; The Human Pangenome Project: a Global Resource to Map Genomic Diversity. Nature 2022, 604, 437-446. [CrossRef]
  3. Rachel M. Sherman; Steven L. Salzberg; Pan-genomics in the Human Genome Era. Nat. Rev. Genet. 2020, 21, 243-254. [CrossRef]
  4. Jordan M. Eizenga; Adam M. Novak; Jonas A. Sibbesen; Simon Heumos; Ali Ghaffaari; Glenn Hickey; Xian Chang; Josiah D. Seaman; Robin Rounthwaite; Jana Ebler; Mikko Rautiainen; Shilpa Garg; Benedict Paten; Tobias Marschall; Jouni Sirén; Erik Garrison; Pangenome Graphs. Annu. Rev. Genom. Hum. Genet. 2020, 21, 139-162. [CrossRef]
  5. 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. [CrossRef]
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Subjects: Biochemistry & Molecular Biology
Contributor MDPI registered users' name will be linked to their SciProfiles pages. To register with us, please refer to https://encyclopedia.pub/register : Yu Peng
View Times: 4
Entry Collection: Molecular Biology and Gene Expression Regulation
Revisions: 2 times (View History)
Update Date: 24 Oct 2026
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