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. 2023 Oct 6;14:6259. doi: 10.1038/s41467-023-42029-4

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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 licence, and indicate if changes were made. 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/4.0/.

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Fig. 1 — a Geographic distribution of 32 selected ecotypes of A. thaliana. The red circles represent non-relict ecotypes while the blue circles represent relict ecotypes. b Phylogenetic tree of 32 A. thaliana ecotypes with A. lyrata as the outgroup. Bootstrap values (%) are displayed on each branch. The red branches represent non-relict ecotypes while the blue branches represent relict ecotypes. c Pan-genome and core genome size simulated by gene cluster number and pan-genome composition. The upper and lower edges of the boxes represent the 75% and 25% quartiles, respectively, while the central line denotes the median, and the whiskers extend to 1.5× the inter-quartile range (IQR). The sample size was set to 1000 and the sample repeat was set to 30. d Number and percentage of core, softcore, dispensable, and private gene clusters. e Bubble chart of gene ontology (GO) enrichment analysis for core genes. Significance was tested by two tailed Fisher’s exact test method. f Bubble chart for the GO enrichment analysis of variable genes. Significance was tested by two tailed Fisher’s exact test method. g Expression levels of genes belonging to core (n = 709,766), softcore (n = 125,555), and dispensable (n = 50,237) gene families. h Pairwise nonsynonymous/synonymous substitution ratios (Ka/Ks) within core (n = 709,766), softcore (n = 125,555), and dispensable (n = 50,237) genes. The upper and lower edges of the boxes represent the 75% and 25% quartiles, the central line denotes the median, and the whiskers extend to 1.5× IQR in g and h. Source data are provided as a Source Data file.