Fig. 6

Ephedra californica transcriptome analyses. a Cluster map of differentially expressed (DE) genes with a ≥ twofold expression change and good transcriptional support (TPM ≥ 0.95) were considered (n = 407). Each column of the heatmap indicated the twofold changes of each sample with respect to the bract. In blue are upregulated genes and yellow downregulated genes. b Cluster map of only DE coding regions DE. c UpSet plot comparing DE genes up- and down- regulated between young ovulate cones and bracts. This representation is an alternative to a Venn diagram allowing for a better visualization of the sets; each bar is a set showing its size (in number of DE genes and percentage); filled-in circles at the bottom show which set is part of an intersection, lines connecting the filled-in cells show the intersection between the groups. Interestingly, 2.4% of shared genes between young cones and bracts are downregulated in the former and upregulated in the later