Fig. 2

Effects of cmt3a and cmt3b mutations on DNA methylation in meiocyte, microspore and sperm. a Transcript levels in FPKM of rice CMT3a and CMT3b in seedling (Se), roots (Ro), meiocyte (Me), unicellular microspore (UM), sperm (S), egg (E), zygote (Z), endosperm nuclei (En, 1.5 days after fertilization) and globular embryo (GE, 3 days after fertilization) from RNA-seq data. The sperm (Kit-S) in Kitaake background was reported by Anderson et al., (2013). b The pollen grains of wild type and cmt3a and cmt3b mutants were I2-KI stained. Bars = 50 μm. c Violin plots comparing overall cytosine methylation levels of wild type and cmt3a and cmt3b mutant meiocyte (Me), unicellular microspore (UM) and sperm (S). The average methylation levels (white dots) and median values (black bars) in transposable elements (TE) are shown. Values of the methylomes are averages from the two replicates. d Number of differential methylated regions (DMR) in cmt3a and cmt3b relative to wild type. Relative portions in TE (> 500 bp), TEG, gene, and Intergenic regions are indicated by different colors. e Venn diagrams showing overlapping of hypo-CHG DMRs in cmt3a and cmt3b meiocyte (left) and sperm (right) relative to wild type cells. f Box plots of DNA methylation levels of hypo-CHG DMRs in meiocyte (Me) versus microspore (UM) (upper) and sperm (S) relative to microspore (UM) (lower) in wild type, cmt3a (3a) and cmt3b (3b) cells. The significance was calculated with multiple comparison tests. Different letters on top of the bars indicate a significant difference (p < 0.05). g Genome Browser screen captures showing high CHG methylation sites in microspore relative to meiocyte and sperm decreased in cmt3b mutants (highlighted by grey)