Fig. 4: Transcriptome comparisons between meristematic and vegetative tissues.

a Image showing key features of a young Welwitschia plant indicating the position of the basal meristem and the terminal groove from which the strap-like leaves emerge. b Longitudinal section of the apical region of a Welwitschia stem (upper): lf = leaf, bm = basal meristem, sb = origin of strobilus, tg = terminal groove, da = dead apex. Diagrammatic representation of KNOTTED-like homeobox Class 1 (KNOX 1) and ASYMMETRIC LEAVES1 /ROUGHSHEATH2 /PHANTASTICA (ARP) gene expression in a typical plant with determinate leaf growth (lower left) and in Welwitschia (lower right). With determinate leaf growth, there is an antagonistic regulation of KNOX 1 and ARP, which does not occur in Welwitschia, resulting in indeterminate leaf growth (SAM = shoot apical meristem, LP = leaf primordia). c Position of tissues along the leaf axis that were sampled for transcriptome analysis, along with an estimation of the age for each leaf region sampled, based on growth rates observed during the long-term ecological monitoring of naturally growing plants at the Gobabeb Station, Namibia. d Significant upregulated expression of genes in basal meristems compared to young leaf sections (left). The number of genes associated with each category is indicated in brackets after the term description, and enrichment values are indicated by color, as shown in the color scale. GO term enrichment for genes highly expressed in young leaf sections compared with old leaf sections (right). e Weighted gene co-expression network analysis revealed expression differences between basal meristems and young leaf material (MM vs MY). The number of genes in each GO term enrichment category at each node (Fisher’s exact test with two-sided and false discovery rate correction used for calculating P values) are shown by the circle size. The probability that the node contains gene(s) that are controlling differential gene expression between tissues is depicted by node color. The lines connecting each node indicate correlated gene expression between genes. f The enzyme NCED (9-cis-epoxycarotenoid dioxygenase), called NCED4 in Welwitschia, is regulated by differential CHH methylation. Hypomethylated cytosines at CHH trinucleotides in the promoter region of NCED4 (negative values) in particular correlate with increased expression in young leaf sections (MY) compared with basal meristem tissues (MM).