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Fig. 4 | BMC Biology

Fig. 4

From: Dynamic and reversible DNA methylation changes induced by genome separation and merger of polyploid wheat

Fig. 4

DNA methylation variation, TE expression, and expansion during wheat polyploidization. a Expression levels of differentially expressed TEs in NHW, ETW, and RHW (Wilcoxon rank-sum test with double asterisks indicating a significant level of P < 0.01). b Methylation changes of TEs that were expressed specifically in the ETW (yellow line) and NHW (blue line) using all TEs (gray line) as a control. c Overrepresentation of expressed TEs in three TE groups (hypergeometric test, P < 0.05). d An example of TE with increased expression and reduced DNA methylation levels. The box indicates the DMR region. The scales are 0–1 for CG and CHG, 0–0.05 for CHH, and 0–50 for FPKM. e Distribution of TEs in NHW relative to NTW and D-genome diploid in A (red), B (green), and D (blue) subgenomes. f Overrepresentation of five TE groups in A (red), B (green), and D (blue) subgenomes. g CG methylation density plots showing an increase in the upstream and downstream regions of the TEs in NHW relative to NTW (blue) and D-genome diploid (purple). Shared TEs in NHW and NTW are used as a control. h Distribution of TEs in upstream, downstream, and gene body. i Percentage of DEGs with TE insertions in upstream, downstream, and gene body using all expressed genes as a control. Double asterisks indicate a significance level of P < 0.01 (hypergeometric test)

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