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. 2024 Nov 13;636(8043):654–662. doi: 10.1038/s41586-024-08187-1

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© The Author(s) 2024

Open Access This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if you modified the licensed material. You do not have permission under this licence to share adapted material derived from this article or parts of it. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by-nc-nd/4.0/.

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Extended Data Fig. 2 — (a) Assembly statistics of 76 chromosome-scale reference genome sequences. (b) Counts of presence/absence variants. (c) Counts of inversion polymorphisms spanning 2 kb or more. (d) Selection of threshold based on pairwise differences (number of SNPs per Mb) for the binary classification into similar/dissimilar haplotypes. (e) The proportion of samples with a close match to one of the 76 pangenome accessions is shown for plant genetic resources (PGR) and elite cultivars in sliding windows along the genome (size: 1 Mb, shift: 500 kb). (f) Distribution of the share of similar windows in individual PGR and cultivar genomes.