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Updated: Dec 14, 2025

Novel Sequence Discovery by Subtractive Genomics
Published on: January 25, 2019
Plant pan-genomes are the new reference
Philipp E Bayer1, Agnieszka A Golicz2, Armin Scheben3
1School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, Western Australia, Australia.
Abstract:
Recent years have seen a surge in plant genome sequencing projects and the comparison of multiple related individuals. The high degree of genomic variation observed led to the realization that single reference genomes do not represent the diversity within a species, and led to the expansion of the pan-genome concept. Pan-genomes represent the genomic diversity of a species and includes core genes, found in all individuals, as well as variable genes, which are absent in some individuals. Variable gene annotations often show similarities across plant species, with genes for biotic and abiotic stress commonly enriched within variable gene groups. Here we review the growth of pan-genomics in plants, explore the origins of gene presence and absence variation, and show how pan-genomes can support plant breeding and evolution studies.
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