DOE Joint Genome Institute

Our Projects
Home › CSP Plans

Early Diverging Lineages of Fungi

Fungi inhabit most of the world’s ecological niches where they perform numerous services that are central to ecosystem functioning. Despite significant advancements in our understanding of the evolutionary relationships within Kingdom Fungi, the earliest diverging events are still very poorly understood. Resolving the earliest branches in the Kingdom Fungi is essential to identify the characteristics… [Read More]

Snow Algae Comparative Genomics

Temperature is one of the most important abiotic determinants of the vitality, viability and distribution of life forms and therefore the biology of cold-adapted organisms is of broad general interest. As polar temperatures rise, the permanent frozen portion of the Arctic is shrinking, as is the geographical region with a summer average of 10ºC, which… [Read More]

How Ascomycetes Degrade Plant Biomass

Aspergilli are generalist species that are able to consume a broad range of substrates. In contrast, species such as P. anserina are much narrower in their substrate utilization profile, which correlates with its biotope on herbivore dung. The soil fungus T. reesei is an intermediate species, which has a broader biotope range than P. anserina,… [Read More]

Modeling Brachypodium-Trichoderma symbiosis

Secondary metabolites are a heterogeneous group of natural compounds that are considered to aid the producing organism in survival and basic functions. Trichoderma spp. are known to produce over 200 secondary metabolites, of which many have been found to have biological activity on plants, microbes and substrates. Among these metabolites, polyketides have important biological activities… [Read More]

Intermediate Wheatgrass Project

Intermediate Wheatgrass (IWG) is a highly productive perennial grass species that is being developed as a new biomass and grain crop. As a perennial crop, IWG can provide essential ecosystem services to current agricultural practices such as stabilizing soil with its deep root structure, reducing nutrient runoff, and limiting weed growth. IWG produces biomass quantities… [Read More]

Fungal Evolution of Truffle-Like Bodies

The reproductive success of fungi is heavily influenced by climate. For those fungi that produce emergent mushroom-like fruit bodies, periods of drought or heat can severely curtail the spread of these fungi within an ecosystem due to rapid drying of the developing hymenium thus limiting spore production and dispersal. Some fungi have evolved the adaptation… [Read More]

Diurnal Cycles in Chlamydomonas

Chlamydomonas reinhardtii is a DOE JGI flagship species and the premier reference organism for unicellular green algae. It is an important reference system for many aspects of plant cell and molecular biology, especially as they relate to energy and carbon metabolism including lipid and starch storage and utilization in photosynthetic systems. Chlamydomonas offers an unprecedented… [Read More]

Microbial Mutualism with Orchids

Mycorrhizal fungi usually transfer nitrogen and phosphorus to plants, and receive carbohydrates. However, the orchid mycorrhizal symbiosis is unique because the mycorrhizal fungi transfer carbon to the plant, at least during early developmental stages. All orchids are dependent on fungi for seed germination and form mycorrhizae with basidiomycete fungi. These mycorrhizal fungal species are primarily… [Read More]

Systems Analysis of Sorghum-Soil Microbiome Interactions

To compete in the energy market, biofuel feedstocks need to be high yielding and carbon neutral or negative. To avoid competition with existing food production systems, these crops will need to be grown on marginal lands with few inputs. Researchers plan to take a systems approach to dissect complex genotype by environment interactions in the… [Read More]

Single Cell Genomics for Station ALOHA samples

Research over the past half-century has built a coherent, conceptual framework for biogeochemical dynamics in natural microbial ecosystems, but quantitative biological and systems biology approaches are only just now beginning to be applied to natural microbial systems. In this project, the researchers intend to apply genome-enabled quantitative systems biology approaches to describe the model open… [Read More]