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    Screencap of green algae video for PNAS paper
    Green Algae Reveal One mRNA Encodes Many Proteins
    A team of researchers has found numerous examples of polycistronic expression – in which two or more genes are encoded on a single molecule of mRNA – in two species of green algae.

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    Advances in Rapidly Engineering Non-model Bacteria
    CRAGE is a technique for chassis (or strain)-independent recombinase-assisted genome engineering, allowing scientists to conduct genome-wide screens and explore biosynthetic pathways. Now, CRAGE is being applied to other synthetic biology problems.

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    Maize can produce a cocktail of antibiotics with a handful of enzymes. (Sam Fentress, CC BY-SA 2.0)
    How Maize Makes An Antibiotic Cocktail
    Zealexins are produced in every corn variety and protect maize by fending off fungal and microbial infections using surprisingly few enzymes.

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    Poplar (Populus trichocarpa and P. deltoides) grow in the Advanced Plant Phenotyping Laboratory (APPL) at Oak Ridge National Laboratory in Tennessee. Poplar is an important biofuel feedstock, and Populus trichocarpa is the first tree species to have its genome sequenced — a feat accomplished by JGI. (Image courtesy of Oak Ridge National Laboratory, U.S. Dept. of Energy)
    Podcast: Xiaohan Yang on A Plantiful Future
    Building off plant genomics collaborations between the JGI and Oak Ridge National Laboratory, Xiaohan Yang envisions customizing plants for the benefit of human society.

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    Expansin complex with cell wall in background. (Courtesy of Daniel Cosgrove)
    Synthesizing Microbial Expansins with Unusual Activities
    Expansin proteins from diverse microbes have potential uses in deconstructing lignocellulosic biomass for conversion to renewable biofuels, nanocellulosic fibers, and commodity biochemicals.

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    High oleic pennycress. (Courtesy of Ratan Chopra)
    Pennycress – A Solution for Global Food Security, Renewable Energy and Ecosystem Benefits
    Pennycress (Thlaspi arvense) is under development as a winter annual oilseed bioenergy crop. It could produce up to 3 billion gallons of seed oil annually while reducing soil erosion and fertilizer runoff.

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    Artistic interpretation of CheckV assessing virus genome sequences from environmental samples. (Rendered by Zosia Rostomian​, Berkeley Lab)
    An Automated Tool for Assessing Virus Data Quality
    CheckV can be broadly utilized by the research community to gauge virus data quality and will help researchers to follow best practices and guidelines for providing the minimum amount of information for an uncultivated virus genome.

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    Unicellular algae in the Chlorella genus, magnified 1300x. (Andrei Savitsky)
    A One-Stop Shop for Analyzing Algal Genomes
    The PhycoCosm data portal is an interactive browser that allows algal scientists and enthusiasts to look deep into more than 100 algal genomes, compare them, and visualize supporting experimental data.

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    Artistic interpretation of how microbial genome sequences from the GEM catalog can help fill in gaps of knowledge about the microbes that play key roles in the Earth's microbiomes. (Rendered by Zosia Rostomian​, Berkeley Lab)
    Podcast: A Primer on Genome Mining
    In Natural Prodcast: the basics of genome mining, and how JGI researchers conducted it in IMG/ABC on thousands of metagenome-derived genomes for a Nature Biotechnology paper.

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    Image of Octopus Springs for the CSP annual call
    Letters of Intent are due April 12, 2021 for the annual Community Science Program (CSP) call focused on large-scale genomic science projects that address specific areas of special emphasis and exploit the diversity of JGI capabilities.

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    SIP engagement webinar
    “SIP technologies at EMSL and JGI” Webinar
    The concerted stable isotope-related tools and resources of the JGI and the Environmental Molecular Sciences Laboratory (EMSL) may be requested by applying for the annual “Facilities Integrating Collaborations for User Science” (FICUS) call.

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    CSP Functional Genomics Call Ongoing
    The CSP Functional Genomics call helps users translate genomic information into biological function. Proposals submitted by July 31, 2021 will be part of the next review.

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    Aerial photo of the switchgrass diversity panel late in the 2020 season at the Kellogg Biological Station in Michigan. (Robert Goodwin)
    A Team Effort Toward Targeted Crop Improvements
    A multi-institutional team has produced a high-quality reference sequence of the complex switchgrass genome. Building off this work, researchers at three DOE Bioenergy Research Centers have expanded the network of common gardens and are exploring improvements to switchgrass.

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    Artistic interpretation of how microbial genome sequences from the GEM catalog can help fill in gaps of knowledge about the microbes that play key roles in the Earth's microbiomes. (Rendered by Zosia Rostomian​, Berkeley Lab)
    Uncovering Novel Genomes from Earth’s Microbiomes
    A public repository of 52,515 microbial draft genomes generated from environmental samples around the world, expanding the known diversity of bacteria and archaea by 44%, is now available .

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    Green millet (Setaria viridis) plant collected in the wild. (Courtesy of the Kellogg lab)
    Shattering Expectations: Novel Seed Dispersal Gene Found in Green Millet
    In Nature Biotechnology, a very high quality reference Setaria viridis genome was sequenced, and for the first time in wild populations, a gene related to seed dispersal was identified.

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Our Projects
Home › CSP Plans
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September 22, 2017

Molecular Mechanisms of Parasitic Chytrids

Chytrids hinder algal biofuel cultivation by causing population crashes, but little is understood about how and under what conditions chytrids infect algae. Recently, researchers have found that the chytrid Paraphysoderma sedebokerense is a facultative algal parasite of Haematococcus pluvialis, whose trophic strategy is regulated by dissolved organic carbon availability. The molecular changes underlying its switch… [Read More]

September 22, 2017

Dynamics of Wetland Mangrove Ecosystems

Wetland mangroves are among the most productive ecosystems on the planet, generating a substantial amount of methane each year. Researchers know very little about how the microbial communities responsible for methanogenesis respond to climatic shifts. Since these communities experience strong subtropical seasonal and diurnal changes in light and temperature, the team aims to track temporal… [Read More]

September 22, 2017

Elucidating Viral “Dark Matter”

This proposal seeks to study viruses and microbes in nearly unexplored extreme environments including hydrothermal vents, glacial sea ice, and modern and ancient sea brines. The team will develop catalogs of which viruses are there, and use these to explore their genomes to identify genes the viruses have ‘stolen’ to augment a key microbial metabolism… [Read More]

September 22, 2017

Microbial Success in Legume-Rhizobia Mutualism

Recent advances have revealed the importance of microbes on plant and animal health. For plant productivity, no microbe-plant association is more important than that between rhizobia bacteria and legume plants. This symbiosis is the major natural contributor of nitrogen, a nutrient that limits plant growth in agricultural and natural systems. This work will identify genes… [Read More]

September 22, 2017

Quantifying Cyanobacteria Interactions

Yellowstone National Park, Octopus hot spring biofilms (Courtesy of Devaki Bhaya)Photosynthetic microbes play a major role in the Earth’s complex biogeochemical cycles. The vast populations of photoautotrophic cyanobacteria in the oceans, terrestrial and freshwater environments fix significant amounts of carbon and nitrogen. These phototrophic hosts are prey to viruses that release carbon and other nutrients, so the long term objective is to quantify dynamic interactions… [Read More]

September 22, 2017

Iron- and Sulfur-Oxidizing Sediment Bacteria

Iron and sulfur are important elements to all life on Earth. Some groups of bacteria use iron and sulfur as energy sources and make organic carbon (sugars) from carbon dioxide in the atmosphere. These bacteria, known as iron- and sulfur-oxidizing bacteria, are found in the sediments and waters of the ocean and on land. They… [Read More]

September 22, 2017

Dynamic Behavior of Soil Ecosystems

By incubating soil with position-specific 13C-labeled glucose and determining the isotope distribution in the pyruvate that is produced, researchers will distinguish between two forms of glycolysis that may occur in intact microbial communities. Additionally, they will sequence DNA and RNA from soils and use that information to improve metabolic models. Improved understanding of microbial energy… [Read More]

September 22, 2017

Metabolic Diversity Across the Great Lakes

The Laurentian Great Lakes hold 20 percent of Earth’s surface freshwater and provide inestimable ecosystem services, yet surprisingly little is known about the structure and activity of microbial communities in this ecosystem. This project seeks to characterize the metabolic diversity and activity of microbes across the Great Lakes, and to understand how these microbes control… [Read More]

September 22, 2017

Gene Expression in Phlebiopsis gigantea

This project seeks to exploit the unique ability of the fungus Phlebiopsis gigantea to rapidly colonize freshly cut loblolly pine. Investigations will advance understanding of the early and exclusive deconstruction of coniferous wood by P. gigantea, provide a framework for functional analyses of hitherto unknown proteins, develop effective biocontrol strategies against economically important root rot… [Read More]

September 22, 2017

Genus-Wide Genomics of Trichoderma

Trichoderma is a genus of fungi that has a broad impact on mankind. There are approximately 270 species of Trichoderma fungi that have varied interactions with other fungi, animals, plants, and efficiently degrade plant biomass material. One species in particular (T. reesei) is well-established for production of enzymes used in the biofuel and biorefinery industries…. [Read More]
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