YIA-PGR: Tools for Plant Comparative Genomics

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The diversity of model systems presents both challenges and opportunities for applying comparative and phylogenetic approaches to questions in plant functional genomics. New methodologies are needed in order to describe features of biological sequences and maps across multiple organisms that are related by a known phylogeny, as opposed to making either simple pair-wise comparisons or 'flat' comparisons among multiple organisms that ignore the presence of phylogenetic structure. This research focuses on two test applications of phylogenomics: (1) identifying conserved motifs and residues that define particular lineages within a gene family and (2) reconstructing genome rearrangement events along a phylogeny in such a way as to be able to predict gene content and order in sparsely sampled genomes. Because some of the methodology proposed is computationally intensive and requires the integration of data from a variety of public sources, this work is complemented by the development of an online plant phylogenomics database called Phytome. In collaboration with the Partnership for Minority Advancement in the Biosciences, an inquiry-based K-12 educational module is developed and delivered to targeted public schools in North Carolina through a mobile science teaching laboratory. Information regarding all the deliverables for our Plant Genome Project willbe posted at the following URL:http://www.phytome.org