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

What makes a tree a tree? Everything that we make from oil could also be made from trees, and trees therefore represent a sustainable and renewable source of biomass for traditional and future industries. Forests are also the world´s largest terrestrial carbon sink. Despite the vital importance and vast potential of forests, we still cannot answer the most fundamental question: What makes a tree a tree? However, we know that trees largely contain the same genes as other plants. To understand what distinguishes trees from other plants, we therefore cannot simply search for unique «tree genes». We need to understand the program that governs where and when genes are turned on and off - we need to understand their regulatory network. The Norwegian Research Council´s basic research program (FRIPRO) has funded the project EVOTree that maps the regulatory network of trees. The project is headed by Torgeir R. Hvidsten, KBM, NMBU and is a collaboration with researchers at Umeå University, Sweden and Ghent University, Belgium. The goal of the project is to describe the regulatory network that orchestrates the differentiation of stem cells into woody tissues and that gives rise to new growth in the tree stem every summer (year rings). We have therefore collected samples from six different tree species and with high resolution quantified where in the year ring the genes in these species are turned on and off. We have also developed advanced data analysis methods to model gene regulation from this data, and to compare these models between different tree species. In parallel, we have also compared the genes of 36 plant species with characterized genomes. The ancestor of these species was a tree, and we can therefore identify «tree genes» by searching for genes that are lost or changed in the 12 species that today are annual herbaceous plants. Taken together, EVOTree will shed light on the evolution of wood development in tree, and describe gene regulation in species as different as aspen and spruce - separated by more than 200 million years of evolution. In addition to providing basic insight into evolutionary processes, the project will produce models that can guide future breeding of better trees with respect to climate adaptation, growth and wood quality.

Everything that we make from oil could also be made from wood. However, despite the vital importance and vast potential of forests, we still cannot answer the most fundamental question: What makes a tree a tree? Nevertheless, comparative genomics have in recent years dramatically increased our understanding of the evolutionary history and architecture of plant genomes, and revealed a remarkable difference in genome size and composition. From these studies we know that gene content varies comparatively little – even between trees and non-tree species – and changes in gene regulation have now emerged as the primary explanation for the evolution of woody plants. In this project, we aim to model the regulatory networks orchestrating the differentiation of stem cells into woody tissues in order to understand the wood formation process in several angiosperms and gymnosperms – the two tree-containing plant lineages separated by over 200 million years of evolution. We will compare regulatory networks to identify specific regulatory mechanisms that separate the two tree lineages from each other and trees from non-tree plants, and we will experimentally test some of the most interesting findings. Modeling approaches such as machine learning are often hampered by the vast number of interacting genes giving rise to complex biological systems. Here we will generate extensive data set on gene regulation and integrate these with prior knowledge in order to infer and align networks across species. This will require highly interdisciplinary research including the development of new computational frameworks and the application of advanced molecular profiling techniques in non-model organisms. This project will deliver both mechanistic insight into the evolution of gene regulation in angiosperm and gymnosperm tree species as well as conserved regulatory mechanisms of great interest to academic researchers and forest industry alike.