Comparative regulomics of wood formation across dicot and conifer trees

Understanding the regulatory program underlying wood formation is key to improving biomass production and carbon sequestration in trees. However, how wood formation evolved and how these programs have been rewired across lineages remains unclear. Here, we present the first high-spatial-resolution evo-devo resource for wood transcriptomes spanning multiple dicots and conifers, representing the two major tree-containing lineages separated by more than 300 million years of evolution. Using orthology-aware co-expression network analysis, we identified genes with conserved and lineage-specific expression patterns. By integrating chromatin accessibility data and transcription factor motif analysis, we further inferred candidate regulatory networks for xylem differentiation and secondary cell wall formation. We demonstrate how this dataset can be used to answer long standing questions in wood biology related to differences in acetylation of cell wall polymers and master regulators of xylem specification across dicot and conifer tree species. The data offer a resource for the tree biology and evo-devo communities, and are publicly available at PlantGenIE.org.