Fig. 3

Association between mRNA level and sRNA level depends on the strand specificity of the sRNA. a Plot of sRNA abundance against mRNA expression level. The grey “x” represents genes that were not differentially expressed. Dots of different colors represent differentially expressed genes with different mRNA inheritance patterns. Blue, HP; grey, MP; orange, LPMP; red, LP. Genes were divided into two groups based on their mRNA abundance, “group I” (RPK < 1000) and “group II” (RPK > 1000). Group II genes showed significant positive correlation between sRNA level and mRNA level. b Percentage of genes with gene body TEs in “group I” and “group II” genes. c Percentage of sense strand sRNA for genes in “group I” and “group II”. **,P < 0.01. d mRNA inheritance is correlated with sRNA strand-specificity. High parent inherited genes (a) show statistically significant enrichment for sense-strand specific sRNA, other inheritance patterns (b) show roughly equal levels of sRNA from the two strands. e Genes with more than 90 % of small RNA from the sense strand (sense > 90 %) show more CG methylation in the gene body. f mRNA inheritance pattern and DNA methylation pattern. HP, high-parent; LP, low-parent; LPMP, between LP and MP; MP, mid-parent; sRNA: small RNA