Comparative analysis of gene regulatory networks identifies conserved regulators in seed plants

Abstract Gene regulatory networks (GRNs) based on transcription factors (TFs) control development and environmental responses. In this study, GRNs were inferred computationally using random forest decision tree-based regression. Networks were constructed for the grasses barley, maize, wheat, brachypodium, sorghum and rice. When compared with Arabidopsis thaliana and alga networks, they show substantial conservation. The degree of conservation depends on phylogenetic closeness. The processes are conserved between all species include basic cellular functions while the processes conserved only in the grasses are annotated with more specific gene ontology terms. In the three species with a carbon concentration mechanism, photorespiration is partially dissociated from photosynthetic regulation. In contrast, in the C4 species, the regulation of C4 genes is associated with photosynthetic regulation. The comparative analyses reveal conserved TFs that control photosynthesis in seed plants but not in the alga. The analyses resulted in a pipeline for the general transfer of information between the small dicot A. thaliana and the commercially relevant grasses.