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. 2023 Apr 6;55(5):852–860. doi: 10.1038/s41588-023-01340-y

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© The Author(s) 2023

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, 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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 2 — a, Modeling of pangenome and core-genome sizes when incorporating additional genomes into clustering and composition of the tomato super-pangenome (pie chart). b, Number of different types of structural variants within each genome compared with the S. galapagense reference genome. c, Distribution of structural variants from the 12 tomato genomes across the 12 chromosomes. d, A wild-specific genomic fragment on chromosome 1. An 8-kb sequence was present in genomes of all nine wild tomatoes but absent from the three domesticated tomatoes. The 8-kb wild-specific region harboring two genes is outlined in red. e, Dot plots display the alignments of chromosome 3 between the 12 tomato genomes and the S. galapagense genome. A clade IV-specific inversion on chromosome 3 from 47.5 Mb to 54.6 Mb is shown, as evidenced by abnormally strong interactions around the inversion breakpoints in Hi-C heat maps. In b, d and e, S. lycopersicum A, S. lycopersicum var. cerasiforme. S. lycopersicum B, S. lycopersicum var. lycopersicum cv. M82. S. lycopersicum C, S. lycopersicum var. lycopersicum cv. Heinz 1706. DEL, deletion; INS, insertion; INV, inversion; TRANS, translocation.

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