Fig. 5: Molecular programmes for environmental responses around recurrent plant hubs.

a–e, Visualization of the co-expression networks clustered by WGCNA into the modules blue (3,101) (a), yellow (1,427) (b), green (1,220) (c), pink (718) (d) and purple (506 genes) (e). Nodes (circles) represent genes connected by edges whose weight (light to dark colour) is based on a weighted TOM. Brightly coloured nodes represent the 20 most connected genes (hubs) and are annotated based on homology; all other nodes are depicted in the corresponding paler colour. Around the clusters, different protein-coding hub genes are highlighted, giving information such as predicted domain structures or phylogenetic relationships; for fully labelled phylogenies, see Supplementary Fig. 26b. Circles in phylogenies give a scale of the ultrafast bootstrap support values; diamonds indicate high (>90%) support for branches separating highlighted clades. An alignment of GLK homologues can be found in Supplementary Fig. 8. f, Using WGCNA, co-expression networks were computed from 212 publicly available RNA-seq datasets from Z. circumcarinatum, M. polymorpha, P. patens and A. thaliana exposed to diverse abiotic challenges, yielding between 12 and 29 modules (labelled above the heat map), and orthogroups for all genes in the modules of these different species were determined. The heat map shows the similarity, based on Jaccard indices, between the modules of Mesotaenium (same colours as throughout the paper, see Fig. 4b) and the co-expression modules in the three land plants as well as Zygnema; red to blue colour gradients indicate high to low Jaccard similarity. g, Cnet plot of the enriched GO terms in the module ‘Arabidopsis 18’, which has high Jaccard similarity to the M. endlicherianum module yellow—note the recurrent terms of plastid operation and, especially, the Clp complex. h, Heat map of the connectivity ranks across all five species for homologues of hub genes of Mesotaenium, from orange (high) to green (low connectivity). Black boxes (top row) indicate if our phylogenies (see data on Zenodo) suggest that the hub genes fall into families that were present in the last common ancestor of Zygnematophyceae and land plants, and hence emerged before plant terrestrialization; white boxes signify the absence of such indication and grey boxes highlight ambiguous relationships.