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. 2022 Sep 24;13:5619. doi: 10.1038/s41467-022-33366-x

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© The Author(s) 2022

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. 3 — a The strategy of genome sequencing and assembling. b The average long-read coverage distribution among strains. c The average read length distribution among strains. d The distribution of contig N50 length among genomes. e The proportional distribution of repeat sequences. f BUSCO evaluation values. g Evaluation of pan-gene plateau. The black curves are fitted with actual data, and the yellow dotted curves are extrapolated by the model of y = A + Be^Cx. The pan-genes obtained from 80, 90, and 100 genomes are similar. h Counts of pan-gene (green) and core-gene (orange) with increased samples. i Comparisons of gene counts between wild, local, improved, and genetic stock groups. j Frequency of gene number. The pie chart shows the proportion of core, softcore, dispensable, and private genes in those genomes. k, l genes with significant frequency differentiation between wild-local (k) and local-improved comparisons (l). In the two comparisons, genes with significantly increased (red) or reduced (blue) frequencies either in domestication (k) or improvement (l) are shown with different colors.