Fig. 2: Identification of candidate DNG target genes.

a WT and single mutant vs double mutant gene expression. Dots correspond to individual genes. Axes indicate mean TPM values for each set of transcriptomes. The strong DEGs (red dots) have ≥8-fold change in expression in double mutant and an average of ≥10 UMIs in the WT and single mutant. An additional 48 genes (weak DEGs, gray dots) showed evidence of differential expression by less stringent criteria (adjusted p-value ≤ 0.05; ≥2-fold change in expression). Raw (unadjusted) p-values were calculated using DESeq2 and then adjusted for multiple hypothesis testing using Holm’s method. b Total expression of the 58 DEGs as a percent of all measured transcripts. Boxplots indicate the median (horizontal dark line), interquartile range (box), and range (vertical lines) of the measured values. Letters indicate statistical significance: groups not sharing a letter have a significantly different mean (p ≤ 0.05; Tukey’s honest significant difference test). See “Statistics and reproducibility” in the “Methods” section for individual p-values. c Expression patterns of DEGs in each pollen grain. Each row represents a single gene, and each column a pollen grain, organized by genotype. Rows are sorted by chromosome, position, and TPM, with genes in clusters listed above singletons. d MaizeGDB browser image of an approximately 30 Kb part of a beta expansin gene cluster on chromosome 5. Included are publicly available DNA methylation tracks and anther gene expression tracks³⁵.