Cluster analyses based on genome-wide cytosine methylation, SNPs and gene expression profiles of the four rice samples. (a) Methylation tree for each sequence context. (b) Genomic tree based on SNPs. (c) Expression tree. Methylation and expression trees were constructed using the distances of correlation coefficients (r) of whole-genome methylation and expression profiles, respectively, among the samples. (d) Relationship between methylation level and their variation among species. The x-axis indicates the log2 transformed methylation level of each sliding-window, and y-axis indicates the log2 transformed CV of corresponding region among four samples.