Additional file 1: of Effects of ploidy variation on promoter DNA methylation and gene expression in rice (Oryza sativa L.)

Figure S1. Graphical output of CyMATE. (A) In silico analysis of methylation of LOC_Os01g59320 in haploid with CyMA. (B) In silico analysis of methylation of LOC_Os01g59320 in diploid with CyMATE. (C) In silico analysis of methylation of LOC_Os01g59320 in triploid with CyMATE. CyMATE filled symbols represent cytosine methylation, while open symbols represent lack of methylation. The sequence context is distinguished by red circles for mCG (Class 1), blue squares for mCHG (Class 2) and green triangles for mCHH (Class 3). Figure S2. Average expression level in 1X, 2X, and 3X. Effect of methylation on gene expression in different gene regions haploid, diploid and triploid seedling, where 1X, 2X, and 3X represents haploid, diploid and triploid plants. (ZIP 1892 kb)补充图S1 CyMATE的可视化输出结果。(A) 利用CyMATE对单倍体中LOC_Os01g59320的甲基化进行计算机模拟分析；(B) 利用CyMATE对二倍体中LOC_Os01g59320的甲基化进行计算机模拟分析；(C) 利用CyMATE对三倍体中LOC_Os01g59320的甲基化进行计算机模拟分析。其中，实心符号代表胞嘧啶甲基化，空心符号代表未发生甲基化；不同序列上下文的甲基化类型通过符号区分：红色圆圈对应mCG（Class 1）、蓝色方块对应mCHG（Class 2）、绿色三角对应mCHH（Class 3）。 补充图S2 1X、2X、3X样本的平均基因表达水平。单倍体、二倍体和三倍体幼苗不同基因区域的甲基化对基因表达的影响，其中1X、2X和3X分别代表单倍体、二倍体和三倍体植株。（ZIP 1892 kb）