SHOAL: Signaling Hubs in the clOsest Algal relatives of Land plants

• Applicant: Professor Dr. Jan de Vries
• Subject Area: Evolution and Systematics of Plants and Fungi ; General Genetics and Functional Genome Biology
• Term: since 2023
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 514060973

Land plants evolved from streptophyte algae in a singular evolutionary event. Meticulous phylogenomic analyses have now consistently recovered the Zygnematophyceae as the closest algal sister lineage to land plants. Recently, and in close succession, four genomes of representative species from the Zygnematophyceae (three of those are Zygnematophycidae) have become available. While this is a significant advance, our exploration of the functional gene space in these genomes is, for now, limited to mere homology. In this project, we will make use of the robust phylogenetic framework that has solicited the Zygnematophyceae as the closest algal relatives to land plants and the recent surge in genome data for these organisms in a co-expression network approach to understand the origin of functional modules. Comparative genomics have shown that decisive hub genes (nodes) of gene regulatory networks salient to defining features of land plants have deep homologs in streptophyte algae — and especially in the Zygnematophyceae; this is the case for signaling genes for (i) auxin, (ii) ethylene, (iii) jasmonate, salicylate and N-hydroxy pipecolic acid, (iv) abiotic stresses and (v) biotic interactions, such as the response to MAMPs or the presence of symbiotic or pathogenic fungi. Using co-expression networks, we will probe the wires (edges) between these hub genes. We will test the hypothesis that core plant-specific functions are built around conserved hubs of orthologous groups of co-regulated genes. Co-expression networks allow us to use the homology-based inferences as beacons for a guilt-by-association approach to explore gene neighborhoods for linking homology-based knowns with unknowns. We here propose to generate the required transcriptome data to construct such networks. Building on and comparisons to functional modules established in land plant model systems, we will dissect these networks for predicted hallmark functions of land plants. Our data will establish a framework for studying the deep evolutionary roots of key plant function. In a meta-analysis, we will test the hypothesis that co-expression (edges) of orthologous genes (nodes) strings together a minimal framework for these key plant functions putatively shared by (i) Zygnematophyceae and established in (ii) land plants. From this minimal framework, the concerted action of genes underpinning defining plant functions of the last common ancestor of land plants evolved.

• DFG Programme: Research Grants