Fig. 5

Analyses of the relationship between m⁶A methylation with expression levels of the target gene in rice under plant virus infection. A Euclidian distance (ED) coefficients among gene expression profiles generated by RNA-seq analysis of the two biological replicates of the three treatments. RNA-seq was performed simultaneously with m⁶A-IP-seq with total RNA extracted at 60 dpt. A lower value means a closer ED of the two compared objects, and with higher reproducibility of the two replicates. B The percentage of rice m⁶A methylated and un-methylated genes at a defined FPKM levels (< 1, 1–5, and > 5). Different colour densities indicate different percentages of the corresponding gene. C Comparisons of number of non-m⁶A methylated genes and number of m⁶A methylated genes in their gene bodies with high (FPKM > 1) and low (FPKM > 1) expression levels in the three treatments. Relationships between gene expression and number were tested using the chi-square test. “*” indicate p- value < 0.05, and “**” means p- value < 0.01. D Box plot comparing FPKM expression levels between non-m⁶A methylated genes and m⁶A methylated genes in the three treatments. A two-tailed unpaired Student’s t -test was performed to calculate the p- values of these three treatments