Additional file 1 of Conservation and trans-regulation of histone modification in the A and B subgenomes of polyploid wheat during domestication and ploidy transition

Additional file 1: Figure S1. The relative proportions of raw data mapped to the three subgenomes of hexaploid wheat. (a), (b) and (c) are the H3K4me3 ChIP-seq data, H3K27me3 ChIP-seq data and RNA-seq data, respectively. Figure S2. Visualized correlation coefficients between the two biological replicates of the ChIP-seq data for the two histone markers and peaks of H3K4me3 and H3K27me3 at representative triad genes. (a) AABB components in H3K4me3; (b) Subgenome A in H3K4me3; (c) Subgenome B in H3K4me3; (d) AABB components in H3K27me3; (e) Subgenome A in H3K27me3; (f) Subgenome B in H3K27me3; (g) peaks of H3K4me3 in subgenomes A, B and D (from left to right in each panel); (h) peaks of H3K27me3 in subgenomes A, B and D (from left to right in each panel). Figure S3. Genome and chromosomal distribution of H3K27me3 in all the plant lines used in this study. Denotations are the same as in legend to Fig. 2. Figure S4. Examples of conservation and remodeling of the two histone modifications (H3K4me3 and H3K27me3) shown by integrative genomics viewer (IGV) snapshots. (a) Groups I-IV H3K4me3 histone modification patterns during the WTW → DTW → ETW process. For Group I (conserved), the three possible relationships, namely, A = B, A < B and A > B, in each of the WTW → DTW → ETW steps are presented; Group II shows changes that occurred in DTW and maintained in ETW; Group III shows changes that occurred in DTW and changed further in ETW; Group IV shows changes that only occurred in ETW. (b) Groups I-IV histone modification patterns (H3K27me3) in the TAA10 → ETW → XX329 ploidy transition process. For Pattern I (conserved), all three changing patterns, namely, A = B, A < B and A > B, in each of the TAA10 → ETW → XX329 steps are presented; Pattern II indicates reversible changes that are exclusively dependent on the presence of DD subgenome; Pattern III indicates changes that only occurred in XX329, reflecting prompt trans-subgenome regulation mediated by the presence of a novel DD genome (newly introduced from Aegilops tauchii); Pattern IV indicates changes that occurred in ETW and XX329, suggesting possible distinct functions of the AABB subgenome. Figure S5. Gene Ontology (GO) analyses of group II-IV genes bearing H3K4me3 modification in WTW → DTW → ETW process (a), and their genome and chromosome distributions (b). From the outside to the inside in (b): Group IV, Group III, Group II, and Group I gene distributions: the blue color represents all genes distributed along the chromosomes. The outermost layer is the position information of the chromosome, where yellow denotes the centromeric and pericentromeric region (Proximal (C)), light blue represents the chromosome arm (Interstitial (R2a/R2b)), and the dark blue indicates the end of the chromosome (Distal (R1/R3)). The punctuated innermost red lines represent length of all the seven wheat chromosomes [28]. Figure S6. Gene Ontology (GO) analyses of group II-IV genes of H3K27me3 modifications in the WTW → DTW → ETW process (a) and gene distribution on genome (b). From the outside to the inside in (b) are distribution of the genes categorized to Groups IV, III, II, and I, respectively. Blue color denotes the distribution of all genes along the chromosomes. The outermost layer represents the position information of the chromosome, where pale yellow shows the centromeric and pericentromeric regions (Proximal (C)), light blue represents chromosome arm (Interstitial (R2a/R2b)), and dark blue indicates chromosome end (Distal (R1/R3)). The punctuated innermost red lines represent length of all the seven wheat chromosomes [28]. Figure S7. Gene Ontology (GO) analyses of pattern II-IV genes of H3K4me3 modification in TAA10 → ETW → XX329 process and gene distribution on genome. From the outside to the inside: Pattern IV, Pattern III, Pattern II, and Pattern I gene distributions, then the blue color represents the distribution of all genes along the chromosomes. The outermost layer is the position information of the chromosome, where the pale yellow shows the centromere and the pericentromeric region (Proximal (C)), the light blue represents the chromosome arm (Interstitial (R2a/R2b)), and the dark blue indicates the end of the chromosome (Distal (R1/R3)). The innermost red line represents the length of all the chromosomes. Black arrows indicate genes of pattern IV, which were enriched at the distal end of the long arm of chr1A and chr1B. Figure S8. Gene Ontology (GO) analyses of pattern II-IV genes of H3K27me3 modification in TAA10 → ETW → XX329 process and gene distribution on genome. From the outside to the inside: Pattern IV, Pattern III, Pattern II, and Pattern I genes distribution, then the blue color represents the distribution of all genes along the chromosome. The outermost layer is the position information of the chromosome, where the pale yellow shows the centromere and the pericentromeric region (Proximal (C)), the light blue represents the chromosome arm (Interstitial (R2a/R2b)), and the dark blue indicates the end of the chromosome (Distal (R1/R3)). The innermost red line represents the length of all the chromosomes. Black arrows indicate genes of pattern IV, which were enriched at the distal end of the long arm of chr1A and chr1B. Figure S9. Gene transcription is not positively correlated H3K27me3 in a comparison of A and B subgenomes between WTW → DTW → ETW process and also TAA10 → ETW → XX329 process.