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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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    The genome of the common fiber vase or Thelephora terrestris was among those used in the study. (Francis Martin)
    From Competition to Cooperation
    By comparing 135 fungal sequenced genomes, researchers were able to carry out a broader analysis than had ever been done before to look at how saprotrophs have transitioned to the symbiotic lifestyle.

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    Miscanthus grasses. (Roy Kaltschmidt/Berkeley Lab)
    A Grass Model to Help Improve Giant Miscanthus
    The reference genome for M. sinensis, and the associated genomic tools, allows Miscanthus to both inform and benefit from breeding programs of related candidate bioenergy feedstock crops such as sugarcane and sorghum.

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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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  • User Programs
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    Scanning electron micrographs of diverse diatoms. (Credits: Diana Sarno, Marina Montresor, Nicole Poulsen, Gerhard Dieckmann)
    Learn About the Approved 2021 Large-Scale CSP Proposals
    A total of 27 proposals have been approved through JGI's annual Community Science Program (CSP) call. For the first time, 63 percent of the accepted proposals come from researchers who have not previously been a principal investigator on an approved JGI proposal.

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    MiddleGaylor Michael Beman UC Merced
    How to Successfully Apply for a CSP Proposal
    Reach out to JGI staff for feedback before submitting a proposal. Be sure to describe in detail what you will do with the data.

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    Click on the image or go here to watch the video "Enriching target populations for genomic analyses using HCR-FISH" from the journal Microbiome describing the research.
    How to Target a Microbial Needle within a Community Haystack
    Enabled by the JGI’s Emerging Technologies Opportunity Program, researchers have developed, tested and deployed a pipeline to first target cells from communities of uncultivated microbes, and then efficiently retrieve and characterize their genomes.

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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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    The Brachypodium distachyon-B. stacei-B. hybridum polyploid model complex. (Illustrations credits: Juan Luis Castillo)
    The More the Merrier: Making the Case for Plant Pan-genomes
    Crop breeders have harnessed polyploidy to increase fruit and flower size, and confer stress tolerance traits. Using a Brachypodium model system, researchers have sought to learn the origins, evolution and development of plant polyploids. The work recently appeared in Nature Communications.

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Our Projects
Home › CSP Plans
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August 1, 2015

Developing Colletotrichium genomics resources

The genus Colletotrichum contains at least 150 species divided into nine major clades, and one of the largest is the Colletotrichum acutatum species complex (CAs). Species belonging to this complex are associated with diseases that infect a wide diversity of crop plants worldwide, and some insects as well. Despite being one of the largest lineages… [Read More]

August 1, 2015

Gene expression profiling in bioenergy grasses

Sugarcane and Miscanthus are closely related to the DOE JGI Flagship plant Sorghum and comprise the Andropogoneae, a tribe of highly productive grasses prominent in energy production. Miscanthus is a nascent DOE JGI flagship, pending completion of a reference genome draft. Sugarcanes and Miscanthus are both polyploids with complex genomes, which has limited the use of modern,… [Read More]

August 1, 2015

Acquired immunity in poplar

Populus trichocarpa was the first tree species whose whole genome was sequenced, assembled and annotated by the DOE JGI for bioenergy applications. This project has two major aims: 1) document the evolutionary process (i.e., the accumulation of mutations) that a single poplar tree undergoes during its lifetime; and, 2) examine the hypothesis that perennial plants… [Read More]

August 1, 2015

Columbia River estuary systems biology

River and ocean end members are heavily populated areas subjected to powerful physical forces and vulnerable to the impacts of human activity and climate change. Estuaries buffer the ocean from the effects of land loads of reactive nitrogen, but can also enhance microbial production of the greenhouse gases carbon dioxide, methane and nitrogen dioxide. This… [Read More]

August 1, 2015

Dung fungi as a model system

Fungi are the primary decomposers of organic matter in terrestrial ecosystems. In order to understand decomposition, it is critical to know how species interact and why species identities change during the decomposition process. This project aims to improve understanding of the community basis for fungal decomposition by developing a model system for decomposition using coprophilous… [Read More]

August 1, 2015

Insights into Coral-Symbiodinium symbiosis

Coral reefs are threatened tropical marine ecosystems whose fundamental unit is the reef building coral. A coral colony is a complex community comprised of both the coral host and its associated microbiome, the coral holobiont. The coral microbiome is important in shaping host health but its metabolic contribution to the coral holobiont is poorly understood,… [Read More]

August 1, 2015

Genomic diversity of Pseudomonas

Pseudomonas is a large and heterogeneous genus, and these bacteria exhibit varied lifestyles in a wide range of environments, including soil, water, plant surfaces, and animals. Due to their roles in bioremediation, biological control, diseases of plants and animals, and many other environmental processes, the metabolic capacities and ecological functions of these bacteria have been… [Read More]

August 1, 2015

Driving the carbon cycle in the dark ocean

The oceans contain the largest reservoir of rapidly exchangeable carbon yet also effectively sequester carbon from the atmosphere for thousands of years. The drivers of this delicate equilibrium are the abundant marine microbial communities ubiquitously present in the Earth’s oceans. This project will provide insight into the major metabolic pathways and key carbon compounds involved… [Read More]

August 1, 2015

Insights on uncultured microbes in wastewater

Currently, anaerobic wastewater treatment serves as an essential municipal waste remediation strategy due to its low cost and efficient waste removal, and the production of methane as a sustainable energy source. To effectively enhance process operation for bioenergy recovery, however, researchers need to better understand the microbial ecology of wastewater treatment. Three primary ecological groups–fermenters,… [Read More]

August 1, 2015

Exploiting Actinobacteria genomes

Actinobacteria are ubiquitously distributed in both aquatic and terrestrial ecosystems and have developed diverse lifestyles, as well free living as in association with a wide variety of eukaryotes. Next to Proteobacteria and Firmicutes, Actinobacteria constitute the third most populated phylum among the Bacteria. This project calls for sequencing the genomes of 1,000 environmental isolates (type… [Read More]
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