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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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    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 › Our Projects › Approved User Proposals › Approved Proposals FY11

Approved Proposals FY11

Following are the approved user proposals for fiscal year 2011.

Community Science Program (CSP) Plans

Algae

Proposer Affiliation Organism
Kerfeld, Cheryl DOE JGI Genome and Transcriptome Analyses of Two Extremely Acidophilic and One Neutrophilic Eukaryotic Algal Species with Diverse Mechanism for CO2 Acquisition
Lovejoy, Connie Laval University, Canada Small planktonic single celled eukaryotes from the Arctic Ocean

Plants

Proposer Affiliation Organism
Muehlbauer, Gary University of Minnesota Whole genome shotgun sequencing of the barley genome
Vogel, John USDA-ARS Surveying natural diversity of the model grass Brachypodium distachyon

Fungi

Proposer Affiliation Organism
de Vries, Ronald CBS-KNAW Fungal Biodiversity Centre, the Netherlands Comparative analysis of Aspergilli to facilitate novel strategies in fungal biotechnology
Goodwin, Stephen Purdue University Sequencing of pathogens and extremophiles in the Dothideomycetes
Hibbett, David S. Clark University Community proposal to sequence a diverse assemblage of saprotrophic Basidiomycota (Agaricomycotina)
Jeffries, Thomas Forest Products Laboratory Yeasts of Biotechnological, Taxonomic and Physiological Interest
Martin, Francis INRA, France Exploring the Genome Diversity of Mycorrhizal Fungi to Understand the Evolution and Functioning of Symbiosis in Woody Shrubs and Trees
Pisabarro, Antonio Public University of Navarre, Spain Comparative transcriptomics pipeline for saprophytic basidiomycota
Pringle, Anne Harvard University Comparative transcriptomics of closely related saprotrophic and ectomycorrhizal Amanita species.
Spatafora, Joseph Oregon State University Phylogenomics and the origin and diversification of Kingdom Fungi
Turgeon, Gillian Cornell University Cochliobolus: expanded and deepened
Turk, Martina University of Ljubljana, Slovenia The varieties of the black yeast-like fungus Aureobasidium pullulans: evolution and use in biotechnology

Bacteria/Archaea

Proposer Affiliation Organism
Bertilsson, Stefan Uppsala University, Sweden Genome wide diversity and population genetics in uncultured aquatic bacteria: single cell genomics of the freshwater SAR11 group and the ubiquitous Actinobacteria ac1 lineage
Chistoserdova, Ludmila University of Washington Genomes of fifty methylotrophs isolated from Lake Washington
Eichorst, Stephanie Los Alamos National Laboratory Populating the branches of the Phylum Acidobacteria with relevant soil strains
Eisen, Jonathan DOE JGI Continuation of the Genomic Encyclopedia of Bacteria and Archaea pilot project
Kalyuzhnaya, Marina University of Washington Coupling function to genomics via single-cell phenotyping and genome sequencing
Liu, Wen-Tso University of Illinois Single cells genomics for uncultured Archaea dominating in a terrestrial subsurface aquifer abundantly containing methane
Sievert, Stefan Woods Hole Oceanographic Institute Shedding Light on the Dark: Single-cell Genomics of Uncultivated Epsilonproteobacteria Inhabiting the Subseafloor Biosphere at Deep-Sea Hydrothermal Vents
Stepanauskas, Ramunas Bigelow Laboratory for Ocean Sciences Generating reference genomes for marine ecosystem research: Single cell sequencing of ubiquitous, uncultured bacterioplankton clades
Tsiamis, George University of Ioannina, Greece Unraveling the unique microbial diversity of the Etoliko lagoon in Western Greece through a single cell genomics approach

Metagenomes

Proposer Affiliation Organism
Bryant, Donald Penn State University Metagenomic and metatranscriptomic analysis of anoxygenic, chlorophototrophic microbial mat communities in Yellowstone National Park
Campbell, Barbara University of Delaware Metagenomic and metatranscriptomic analysis of carbon cycling in Delaware coastal waters
Dionisi, Hebe Patagonian National Research Center, Argentina Microbial Community Structure and Metabolic Potential of Chronically Polluted Marine Sediments from Cold Regions of the Northern and Southern Hemispheres
Distel, Dan Ocean Genome Legacy Foundation, Center for Marine Research The complete shipworm microbiome: a comparative genomic and metagenomic analysis of lignocellulose-degrading microbial communities from multiple species of wood-boring bivalves.
Girguis, Peter Harvard University Linking mantle to microbe: a community-wide effort to ally hydrothermal vent microbial identity and ecology to geochemical cycles via metagenomics
Hallam, Steven University of British Columbia, Canada Microbial Systems Ecology of Expanding Oxygen Minimum Zones in the Eastern Subtropical North Pacific Ocean
Kerfeld, Cheryl DOE JGI Metagenomic Sequencing for Understanding Microbial Carbon Cycling by Biological Soil Crusts of Arid Lands
Macalady, Jennifer Penn State University Uncultivated and novel microbial lineages in terrestrial subsurface biofilms from a sulfidic aquifer
McMahon, Katherine University of Wisconsin High-resolution temporal and spatial dynamics of microbially-mediated carbon processing revealed though time-series metagenomics in freshwater lakes
Moran, Mary Ann University of Georgia Transcriptional analysis of a marine bacteria-phytoplankton binary model system
Muyzer, Gerard Delft University of Technology, the Netherlands Metagenomics of microbial communities from soda lakes and soda solonchak soils
Tringe, Susannah DOE JGI Microbial community impact on carbon sequestration in managed wetland “carbon farming”
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  • Approved Proposals FY13
  • Approved Proposals FY12
  • Approved Proposals FY11
  • Approved Proposals FY10
  • Approved Proposals FY09
  • Approved Proposals FY08
  • Approved Proposals FY07
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