Methylation patterns of different types of TEs with different lengths. Read density distribution is shown for DNA-TEs (A), LINEs (B), LTRs (C), and SINEs (D) with length of less than 500 bp (SINEs included four additional subgroups with length of less than 100 bp, 100–200 bp, 200–300 bp, and 300–500 bp), 500 to 2,000 bp, and more than 2,000 bp across different developmental stages of rice embryo and endosperm. The K-S test was performed and revealed a significant difference in the numbers of short DNA-TEs (less than 500 bp) and SINEs (less than 500 bp) between the embryo and endosperm (P < 0.001).