Fig. 3: Genomic impacts of inversions in Curcuma species.
From: Inversions encounter relaxed genetic constraints and balance birth and death of TPS genes in Curcuma
a Comparison of gene expression, nucleotide substitution rates, and LTR content between inversions and genome-wide background in the three Curcuma species. b Comparison of gene expression, nucleotide substitution rates, and LTR content between inversions and high LTR regions in C. alismatifolia. The red dashed line indicated the mean LTR content in inversions (window size = 500 Kbp). The red shaded area indicated the non-inverted region where the LTR content exceeded the mean LTR content in the INTRA. The rhombuses represented the mean. The left y axis of the density map corresponded to INTRA, and the right y axis corresponded to HLR. c Linear regression of gene expression levels (R2 = 0.91, p = 0.001) among genomic regions when departing away from inversions in C. alismatifolia. d Linear regression of nucleotide substitution rates (R2 = 0.84, p = 0.004) among genomic regions when departing away from inversions in C. alismatifolia. e Linear regression of LTR content (R2 = 0.45, p = 0.102) among genomic regions when departing away from inversions in C. alismatifolia. a–e The box-plot elements were defined as: center line, median; box limits, upper and lower quartiles; whiskers, 1.5× interquartile range; points, outliers; rhombuses, mean. a, b Two-sided Wilcoxon rank-sum test was conducted for significance evaluation, and multiple comparisons were adjusted with the Bonferroni correction. Asterisks represented significant differences (***p < 0.001, adjusted, Supplementary Data 5). c–e The R² and p values were shown. FPKM fragments per kilobase of transcript per million fragments mapped, Ka nonsynonymous substitution rate, Ks synonymous substitution rate, LTR-gf The content of LTR in the 3 Kbp flanking regions of genes, INTRA inversions between haplotypes within species, INTER inter-specific inversions among the three species, POP inversions among populations of C. alismatifolia. BK genome-wide background. HLR high LTR regions. Source data are provided as a Source Data file.
