Comparative Genomics Analysis of Gravitropic Response in a Phylogenetic Survey of Angiosperm Trees

The innovation of woody growth in angiosperms is believed to be an ancestral trait that has been highly modified to generate the anatomical diversity seen in different angiosperm lineages. Most angiosperm trees modify woody development in respond to gravity through the production tension wood, which generates tensile force to pull the tree against the gravity vector. Currently, a comprehensive understanding of the genetic pathways underlying wood development and gravitropic responses across angiosperm trees is lacking. In this project, we applied a comparative genomics approach to understand the evolution of gravitropic responses across multiple species of angiosperm trees from the genera Liriodendron, Liquidambar, Eucalyptus, Populus and Salix. We generated gene expression profiles for each species in developing xylem from upright plants, and from the top (tension wood) and bottom (opposite wood) surface of leaning stems. Using a network-based approach that takes into account within species co-expression networks and across species orthologous relationships, we identified a large-scale multi-layer network that aligns co-expression patterns across multiple species. We identified lineage specific gene modules and conserved modules that were defined as groups of orthologous genes that were co-expressed across multiple species. Furthermore, functional annotation of modules suggests that these modules represent specific biological pathways involved in the regulation of hormones, cell-wall biosynthesis, meristem development and epigenetic processes.