Fig. 2

Sample relationship and differential gene expression. A Multidimensional scaling plot of seminal root tissue transcriptomes. B Number of differentially expressed genes (DEGs) identified in each root zone-by-time point combination. Bars represent up-regulated (log₂FC > 1) and down-regulated (log₂FC < -1) DEGs with an FDR < 5%. C Comparison of DEGs across root zones and time points. Intersections are marked by connecting lines between samples. The total number of intersected genes is indicated above each bar. DEGs that are unique to their root zone-by-time combination are marked in black. Intersections of DEGs from the same root zone across different time points are marked in blue, intersections of DEGs from the same time point across different root zones are marked in green, all other intersections are marked in grey. CM: root cap and meristem; EZ: elongation zone; DZ: differentiation zone