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Plant Program

Plant ProgramThe Plant Program focuses on the fundamental biology of photosynthesis, conversion of solar to chemical energy. Other areas of interest include characterizing ecosystems and the role of terrestrial plants and oceanic phytoplankton in carbon sequestration; the role of plants in coping with toxic pollutants in soils by hyper-accumulation and detoxification; feedstocks for biofuels, e.g., next-generation cellulosic biofuels from perennial grasses and forest plantation trees; the ability to respond to environmental change (e.g., loss of diversity from monoculture produces vulnerabilities; nitrogen-fixing nodules in legumes reduce fertilizer need).  In addition, the Plant Program generates useful secondary metabolites (produced largely for disease resistance) for positive/negative control in agriculture, with attendant influence on the global carbon cycle.

Major Plant Program initiatives include:

  • Phytozome, a joint project with the UC Berkeley Center for Integrative Genomics to facilitate comparative genomic studies amongst green plants. Famlies of genes that represent the modern descendants of ancestral gene sets are constructed at key phylogenetic nodes. These families allow easy access to clade-specific relationships as well as clade-specific genes and gene expansions. http://phytozome.archive.jgi.doe.gov
  • Plant Flagship Genomes, are the most important to DOE mission and plant science selected for focusing our computational and experimental efforts to move beyond sequence to function and to provide the most direct benefit for enabling world-class science. Read more.
  • Plant Gene Atlas, a major initiative to develop gene expression catalogues for five species, sampling a wide variety of relevant developmental and experimental conditions (uniform nitrogen application and metabolism, etc.) using deep-coverage RNA-seq methods and small RNA sequencing. In addition to facilitating direct comparisons of gene expression patterns within a species of interest, these data will enable broad inferences of shared gene function across phyla, focusing on applications to address mission-oriented research within DOE relevant plants.  Ultimately the effort will lead to depositing validated, accurate data sets into the DOE’s Biology Knowledgebase (KBase): http://kbase.us/.