Plant Program

The Plant Program advances our understanding of plants’ biological and ecological roles to foster sustainable solutions for energy, agriculture and the environment. At its core, the program investigates photosynthesis — the process that transforms solar energy into chemical energy — and its implications for carbon sequestration, renewable energy and agricultural productivity. Research spans diverse areas — from understanding how terrestrial plants and phytoplankton capture atmospheric carbon, helping to regulate Earth's carbon balance, to exploring the genetic basis of how plants have naturally adapted to varied climate and soil conditions around the globe to identify genes to improve our domesticated species. 

The program supports the development of next-generation biofuels by studying perennial grasses and fast-growing trees as renewable energy feedstocks. It also tackles challenges posed by environmental change, focusing on plant resilience — highlighting the vulnerabilities of monocultures and the benefits of nitrogen-fixing nodules in legumes, which can reduce dependence on fertilizers. The study of secondary metabolites enhances our understanding of natural compounds that support disease resistance, with applications in sustainable agriculture, including the development of complex biomolecules — which can include antimicrobial and anti-pest compounds. 

The program is working to expand genomic resources for key plant species, enhancing our understanding of plant diversity and integrating various data types to explore the molecular mechanisms behind phenotypic evolution. It also utilizes advanced tools, including deep learning algorithms for gene annotation and protein folding models, to improve the accuracy of functional predictions and speed up genome analysis.

Additionally, the Plant Program is advancing research into plant-microbiome interactions, focusing on how environmental stress and microbial communities affect plant growth and productivity. These insights have the potential to inform strategies that improve agricultural yields and support ecosystem health. By integrating cutting-edge technologies and data-driven methods, the program equips researchers worldwide to tackle challenges in energy, agriculture, and environmental sustainability.

• Plant Flagship Genomes are selected through discussion with the JGI Plant Genome Advisory Committee and DOE, designating a set of JGI plant genomes that are the most important to DOE mission and plant science. These species form the basis of plant research in the DOE Bioenergy Research Centers.
• The Plant Gene Atlas initiative develops gene expression catalogs across JGI Plant Flagship speciesspecies, using deep-coverage RNA-seq analyzed in a consistant computational framework. It enables cross-species comparisons, advancing DOE mission-oriented research and contributing validated datasets to further gene function research.
• The Open Green Genomes (OGG) project seeks to develop comparative high quality genomes and annotations across the plant kingdom to enable advanced methodologies for determining gene origin and function. These species are carefully selected by the community to evenly sample the diversity of the plant kingdom and allow ancestral reconstructions of plant genomes.
• With the JGI Plant Flagship Pangenomes, driven by DOE science needs, this program is expanding JGI Plant Flagship genomes into pangenomes, which capture much greater diversity for these species. The pangenomes enable the exploration and identification of small and large structural variation — this variation drives major phenotypic differences in plants and will accelerate gene discovery.
  • BrachyPan on Phytozome
  • PennyPan on Phytozome
  • SorghumPan on Phytozome