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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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October 1, 2019

Genomic Variation in Mustard Family Metabolism

Studies of genomic variation are critical to developing a synthetic, systems and quantitative understanding of how to improve crops. However, modern short-read methodologies may actually miss the very genes that are critical to adapting crops to new environments or making them healthier. This project will create high-quality genomes of multiple crops and species from the mustard family to test new methods and technologies to ensure that these genes essential for adaptation and improvement are identified. [Read More]

October 1, 2019

Fungal Root Endophytes of Soybean

This project investigates fungal root endophytes of the oilseed crop soybean for their potential to deter biotic stresses from root pathogen such as the soybean cyst nematode and the sudden death syndrome fungal root-rot pathogen. [Read More]

October 1, 2019

Expanding Metabolic Understanding of C- and S- Cycling Microbes

Is there more biochemistry to be discovered in the microbial world? How universal is biochemistry between distantly related bacteria? A massive amount of microbial genome data exists, yet every new sequence finds genes for which we cannot predict a concrete function. This proposal seeks to combine genomic information with direct detection of metabolites to answer these questions and provide a path for assigning gene functions in two distantly related microbial groups that play key roles in carbon and sulfur cycling in multiple ecosystems across the planet. [Read More]

October 1, 2019

Scaling Microbial Traits From Genomes to Watersheds

Soil core showing redoximorphic features sampled from watershed zone of high vegetation nitrogen uptake. (Courtesy of Eoin Brodie)Using remote sensing, metagenomics and machine learning, we are building new ways to predict of how plant and microbial metabolism interact to influence biogeochemistry across watersheds in the headwaters of the Colorado River. [Read More]

October 1, 2019

Wood Decay by Soft Rot Fungi

This project seeks to ascertain the mechanisms of lignocellulose deconstruction employed by these soft rot fungi. [Read More]

October 1, 2019

How Black Fungi Adapt to Extremes

Black fungi spread in diverse extreme environments playing a crucial role by recycling organic matter, enabling nutrient uptake. They are also involved in biogeochemical processes, including rock transformations, bioweathering, mineral formation. The STRES project aims to dig into the genome diversity and metabolites involved in stress response to: i) gain insights into the evolutionary processes allowing black fungi to successfully adapt to extremes; ii) clarify their role in the functioning and balance in extreme-ecosystems; iii) explore the role of melanin in energy processes. [Read More]

October 1, 2019

Grass Genes Regulating Bioenergy Relevant Traits

Grass species have a tremendous potential to be engineered to generate biofuels that can feed our economy. A major challenge has been accessing the energy stored in plants. Purple false brome (Brachypodium distachyon), a wild grass species from the Mediterranean region, is a perfect model for testing novel ways of changing plants to help produce biofuels. In this study, researchers are accessing variation in this species to identify genes that could transform bioenergy crops. These resources are openly shared with the scientific community in order to speed up research and transform society. [Read More]

October 1, 2019

Mapping Methanogenic Metabolic Networks

Anaerobic digestion (AD) systems produce methane-rich biogas, which can be upgraded and distributed within the existing energy grid. Despite the widespread adoption of AD for waste management and bioenergy generation, the microbial networks driving methane production from organic matter remain poorly constrained, limiting our capacity to predict impacts of process perturbations. Here, we will combine stable isotope and amino acid tracers with genomic sequencing to determine “who is doing what” in AD, with the overall aim of improving biofuel production efficiency from renewable biomass. [Read More]

October 1, 2019

Microbial Roles in Plant Drought Tolerance in the Sahel

The Sahel region in West Africa is highly vulnerable to drought, endangering the livelihood of millions of millet subsistence farmers in the region. However, a solution has been revealed; when farmers grown millet in close proximity with native woody shrub gueira, the millet has greater biomass and yields. We predict that the millet-associated microbial community is influenced by the shrub such that the microbes are able to confer better drought resistance to their host millet in the presence of the shrub. We will characterize the metagenomes of millet to test this hypothesis. [Read More]

October 1, 2019

Plant-Microbe Interactions of a Wood Decay Fungus

This research project focuses on elucidating the plant-microbe interactions of the wood decay fungus Perenniporia fraxinea, a serious pathogen of hardwood trees. Multi-omics analyses will reveal the comprehensive mechanisms and key fungal genes involved in the wood infection and degradation processes will be identified. Furthermore, key fungal proteins involved in the processes will be biochemically characterized and subjected to chemical screening in our efforts to identify specific inhibitors with potential as novel wood-protective agents against P. fraxinea and related wood-decay fungi. [Read More]
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