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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 FY09

Approved Proposals FY09

Following are the approved user proposals for fiscal year 2009.

Community Science Program (CSP) Plans

Eukaryotes

Organism Proposer Affiliation
Resequencing Trichoderma reesei Scott Baker Pacific Northwest National Lab
Rhizopogon salebrosus (ectomycorrhizal fungus) Thomas Bruns University of California, Berkeley
Ceriporiopsis subvermispora (lignin-degrading fungus) Daniel Cullen USDA Forest Products Laboratory
Gene expression in Chlamydomonas reinhardtii Maria Ghirardi Natl. Renewable Energy Lab.
Paralvinella sulfincola (polychaete worm) Peter Girguis Harvard Univ.
Thalassiosira rotula (diatom) Bethany Jenkins Univ. of Rhode Island
Dendroctonus frontalis (southern pine beetle) ESTs Scott Kelley San Diego State Univ.
Botryococcus braunii (Oil-Producing Green Microalga) cDNA Andrew Koppisch Los Alamos Natl. Lab.
Chlamydomonas and Volvox transcriptomes Sabeeha Merchant Univ. of California, Los Angeles
Spirodela polyrhiza (duckweed) Todd Michael Rutgers
Zostera marina (seagrass) Jeanine Olsen University of Groningen
Gossypium (cotton) Andrew Paterson Univ. of Georgia
Pine BAC Sequencing Daniel Peterson Mississippi State Univ.
Hansenula polymorpha strain NCYC 495 leu1.1 (ATCC MYA-335) Andriy Sibirny Institute of Cell Biology, Ukraine
Resequencing of Brachypodium distachyon John Vogel USDA-ARS Western Regional Research Center
Nanoflagellates: Paraphysomonas, Ochromonas, and Spumella Alexandra Worden Monterey Bay Aquarium Research Institute

Bacteria and Archaea

Organism Proposer Affiliation
Four diverse cellulose degrading microbes Iain Anderson DOE JGI
Escherichia coli MG1655 John Battista Lousiana State Univ.
Sinorhizobium meliloti strains AK83 and BL225C Emanuele Biondi Universita’ di Firenze
Methylotenera species Ludmila Chistoserdova Univ. of Washington
SAR11 Genome Evolution Stephen Giovannoni Oregon State Univ.
Rhodopseudomonas palustris strain DX-1 Caroline Harwood Univ. of Washington
Cycloclasticus pugetii (a PAH-Degrading Bacterium) Russell Herwig Univ. of Washington
Burkholderia sp. Ch1-1 and Burkholderia sp. Cs1-4 William Hickey Univ. of Wisconsin
Sphaerochaeta pleomorpha and Sphaerochaeta globus Frank Loeffler Georgia Inst. of Technology
Archaeal transcriptomes Todd Lowe Univ. of California Santa Cruz
Dehalogenimonas lykanthroporepellens William Moe Louisiana State Univ.
Desulfurococcus (hyperthermophilic archaeon) Biswarup Mukhopadhyay Virginia Bioinformatics Inst., Virginia Polytechnic Inst. and State Univ.
Mesorhizobium ciceri bv biserrulae (strains WSM1271, WSM2073 and WSM2075) (legume symbionts) Kemanthi Nandasena Murdoch Univ.
Thermoacidophiles of deep-sea hydrothermal vents Anna-Louise Reysenbach Portland State Univ.
Alicycliphilus denitrificans strain BC Alfons Stams Wageningen Univ.
Desulfotomaculum species Alfons Stams Wageningen Univ.
Freshwater Actinobacteria belonging to the acI lineage Falk Warnecke DOE JGI

Metagenomes

Organism Proposer Affiliation
Novel subsurface microbial phylotypes Jennifer Biddle Univ. of North Carolina, Chapel Hill
Highly efficient, highly stable, reductive dechlorinating bioreactor Eoin Brodie Lawrence Berkeley National Lab
Bankia setacea (shipworm) metagenome. Daniel Distel Ocean Genome Legacy
Hoatzin crop microbiome Maria Dominguez-Bello Univ. of Puerto Rico
Ammonia-oxidizing archaeal enrichment culture Christopher Francis Stanford Univ.
Subarctic Pacific Ocean Steven Hallam Univ. of British Columbia
Lake Vostok accretion ice Philip Hugenholtz DOE JGI
Microbial communities at the Hanford 300A IFC Site. Allan Konopka Pacific Northwest Natl. Lab.
PCE-dechlorinating mixed communities Ruth Richardson Cornell Univ.
Uncultivated marine viruses Grieg Steward Univ. of Hawaii
Great Salt Lake Bart Weimer Utah State Univ.
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