Section 4: Theme for a New Research Coordination Group on Green Plant Phylogenomics

The goal of this proposal is to establish a new research coordination network to integrate green plant phylogenetics and green plant genomics into a new field that could be called "phylogenomics" (Eisen, 1998). We want to explore the ways in which comparative phylogenetic studies can inform functional genomic studies, and knowledge of plant genomes can inform the understanding of phylogenetic relationships. Both communities of researchers are individually well-coordinated, but there are almost no linkages between them at the present. Genome biologists are very keen on making comparisons among organisms, and are indeed already starting, but are initially proceeding rather naively without taking advantage of current phylogenetic techniques and results. Likewise, most phylogeneticists are naive about just how fast the data are coming from the genomics projects and the power of some of the new technologies. So, both groups of researchers would benefit greatly from increased communication and collaboration.

The present proposal is thus designed to take the previous Deep Green effort to the next level of excellence. We need to continue the activities that are already working well (such as workshops and web-based coordination and data-sharing), but move beyond straight phylogenetic reconstruction and into the area of structural and functional genomics. This will broaden the collaboration to include more of biology, and thus increase the opportunities for interdisciplinary exchange and cross-training.
From the phylogenetics standpoint, we now have a very clear idea of those taxa and characters in greatest need of study, and we propose to develop new genomic-level characters to address the remaining questions in a focused manner. From the genomics standpoint, we will examine new ways in which the comparative framework given by a well-supported phylogeny can be used to direct functional research and interpret data. Such studies will help us to integrate what we are learning from angiosperm genomics into the much broader context of plant genome evolution. At this point we can probably only incompletely grasp the potential research areas that could come out of a full integration of genomics and phylogenetics research. However, by way of providing some examples, in the next section we discuss selected research areas where synergistic benefits are sure to occur.