EVOTREE: What makes a tree a tree? Characterization and evolution of the gene regulatory network underlying wood development

We aim to understand the process of wood formation in angiosperm and gymnosperm tree species by modelling the regulatory networks orchestrating the differentiation of stem cells into woody tissues. We are integrating multi-omics data to infer regulatory networks for each species and comparing these networks across species to identify regulatory mechanisms explaining the evolution of trees. In addition, we will test experimentally some of the predicted regulatory mechanisms.

Approaches
To study the evolution of gene regulation in trees, we will align regulatory networks from three gymnosperm (conifers) and three angiosperm tree species. While each regulatory network will describe co-regulation within a species, their multiple alignment will reveal conserved and diverged regulation across species. We will then study various network properties including individual genes, simple topologies containing several genes (i.e. network motifs), subnetworks (i.e. gene modules), and regulatory mechanisms (i.e. one or more regulators targeting a cis-regulatory module (CRM) of co-expressed genes).

Network properties that align across all or most species are conserved and will reveal core regulatory mechanisms underlying wood formation, while those aligning in only subsets of species have diverged and can be used to explain the evolution of plant diversity. In this project, we are particularly interested in properties with high conservation within gymnosperms and angiosperm trees, but that differ between gymnosperms and angiosperms, since these can explain differences between the two tree lineages. We are also interested in properties conserved across all trees, but that are different in non-tree species such as arabidopsis, since these can answer the question: What makes a tree a tree?