Additional file 3: of DNA methylation footprints during soybean domestication and improvement

Figure S1. Pipeline for WGBS analysis. Figure S2. Genetic diversity difference among different genomic regions. Figure S3. Genetic diversity comparison between DMR, DSR, and NSR in wild, landrace, and cultivar populations. Figure S4. The genetic diversity changes between corresponding populations for increased and decreased DMRs. Figure S5. The genetic diversity comparisons between corresponding populations for domestication DMRs (a) and improvement DMRs (b). Figure S6. Overlap between domestication and improvement DMRs for different cytosine contexts. Figure S7. Relationship of CG and CHG methylation levels for overlapped CG-DMRs and CHG-DMRs. Figure S8. Length comparisons among overlapped CG-DMRs and CHG-DMRs, unique CG-DMRs, and unique CHG-DMRs. Figure S9. Hierarchical clustering of methylation level and corresponding siRNA expression for associated DMR/siRNA pairs in domestication (a) and improvement (b). Figure S10. The genetic diversity difference between TE variant associated DMRs and TE variant not-associated DMRs for different genomic regions. Figure S11. Overlap between overlapped CG-DMRs and CHG-DMRs (O-CG/CHG DMRs) who associated with genetic variations for domestication (a) and improvement (b). Figure S12. Overlap and GO enrichment analysis for genes in “pure Dos_CG-DMRs” and “pure Dos_CHG-DMRs.” Figure S13. The correlation between CG methylation level and expression level for genes in “pure DMRs.” (PDF 3689 kb