Fig. 4: Inversions were depleted with selected SNPs in C. alismatifolia.

a Population structure of 56 C. alismatifolia cultivars at K = 2. g1 and g2 represented two groups with large differences in multiple traits. b Comparison of the proportion of selected SNPs (with 95% percentile as threshold for outliers; two-sided χ² test, ***p < 0.001, Supplementary Data 8) between inversions and non-inversions based on XP-CLR (top), nSL analysis (down). c The polymorphism information content (PIC) of multi-allelic SNPs (≥2 alleles per site) in genes. d Comparison of recombination rates among inversions, high LTR regions, and genome-wide background in C. alismatifolia. c, d The box-plot elements are defined as: center line, median; box limits, upper and lower quartiles; whiskers, 1.5× interquartile range; points, outliers; rhombuses, mean. e Comparison of percentage of deleterious mutations between inversions and genome-wide backgrounds in C. alismatifolia. Deleterious mutations of the top five longest inversions were also shown, where Chr08 stood for “CaChr8-TPS-TD-INV” (8-10517073-28214380), the longest inversion on C. alismatifolia chromosome 8. Additive: the additive mode with deleterious alleles in both homozygous and heterozygous genotypes; Recessive: the recessive mode with deleterious alleles only in homozygous genotypes. CDS: coding sequence. Box-plot elements are defined as: center line, median; box limits, upper and lower quartiles; whiskers, 1.5× interquartile range; points, all values, n = 56. INTRA inversions between haplotypes within species, NON-INV non-inversion region, BK genome-wide background, HLR high LTR regions. c–e two-sided Wilcoxon rank-sum test was employed for significance evaluation, and multiple comparisons were adjusted with the Bonferroni correction. Asterisks represented significant differences (***p < 0.001, adjusted, Supplementary Data 5). Source data are provided as a Source Data file.