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    Sorghum variety BTx642 grown in Central Valley at temperatures around 100 degrees for 65 days without water. It is still green and filling grain to almost the same extent as plants that were watered weekly. (Jeffrey Dahlberg, UC ANR Agricultural Research and Extension Center)
    Dealing with Drought: Uncovering Sorghum’s Secrets
    Sorghum bicolor (L.) Moench is an African grass that adroitly handles droughts, floods and poor soils. This is the first paper that describes sorghum’s response to drought, from a large-scale field experiment led by a multi-institutional consortium to uncover the mechanisms behind sorghum’s capacity to produce high yields despite drought conditions.

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    The lichen Gray’s Cup (Cladonia grayi), with its namesake goblet structures. (Thomas Barlow)
    Making a Lichen Together
    Despite a century-and-a-half of lichen research, many details of lichen symbiosis remain unclear. For the first time, a team has analyzed in parallel the genomes and transcriptomes of both partners to better understand lichen.

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    Poplar cuttings inoculated with M. elongata strain PM193 (far right) grow larger in 30 percent forest soil / 70 percent sand than without PM193 (middle). On the left are controls grown in sterile sand. (Chih-Ming Hsu)
    Fungus Fuels Tree Growth
    Poplar is the fastest growing hardwood tree in the western United States, making it an energy feedstock of particular interest to the U.S. Department of Energy (DOE). The fungus is almost always found among and within poplar trees, and in an effort to understand its influence on the plant, a team of scientists studied what happens to the tree’s physical traits and gene expression when the fungus is present.

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    Jorge Rodrigues is interested in the biological causes of methane flux variation in the Amazon rainforest. (Courtesy of Jorge Rodrigues)
    Methane Flux in the Amazon
    Wetlands are the single largest global source of atmospheric methane. This project aims to integrate microbial and tree genetic characteristics to measure and understand methane emissions at the heart of the Amazon rainforest.

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    Vampirovibrio chlorellavorus in yellow on green host. (Courtesy of Judith Brown)
    Infections and Host-Pathogen Interactions of Chlorella
    The non-photosynthetic, predatory cyanobacterium Vampirovibrio chlorellavorus is a globally important obligate pathogen of Chlorella species/strains, which are of interest as biofuel feedstocks.

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    Morphological diversity of Sordariales growing in the lab. Pierre Gladieux's proposal explores functional diversity in Neurospora and its relatives. (Pierre Gladieux, INRA Montpellier)
    Insights into Functional Diversity in Neurospora
    This proposal investigates the genetic bases of fungal thermophily, biomass-degradation, and fungal-bacterial interactions in Sordariales, an order of biomass-degrading fungi frequently encountered in compost and encompassing one of the few groups of thermophilic fungi.

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    Improving the Cacao Genome and Phytozome
    An updated reference genome for Theobroma cacao Matina 1-6 has now been completed and released by HudsonAlpha scientists, with the help of Mars Wrigley funding. The annotated genome has been updated to a high quality modern standard and includes RNA-seq data. The improved genome is available for comparative purposes on the latest version of the JGI plant portal Phytozome (phytozome-next.JGI.doe.gov).

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    Panorama of Washburn Hot Springs (Yellowstone National Park). Sediments from the upper pool were sampled and subjected to DNA sequencing by the DOE-Joint Genome Institute (YNP Research Permit: YELL-2012-SCI-05068, PI: W. Inskeep. Image: R. Hatzenpichler).
    Expanding Universe of Methane Metabolisms in Archaea
    In Nature Microbiology, researchers mined the Integrated Microbial Genomes & Microbiomes (IMG/M) database maintained by the JGI for publicly available metagenome data provided by the other study co-authors, and reconstructed from these 10 metagenome-assembled genomes (MAGs) representing new potential methanogenic, anaerobic methanotrophic and short-chain alkane-oxidizing archaea.

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    Click on the image above or click here (https://youtu.be/iSEEw4Vs_B4) to watch a CRISPR Whiteboard Lesson from the Innovative Genomics Institute, this one focuses on the PAM sequence.
    Mining IMG/M for CRISPR-Associated Proteins
    Researchers report the discovery of miniature CRISPR-associated proteins that can target single-stranded DNA. The discovery was made possible by mining the datasets in the Integrated Microbial Genomes and Microbiomes (IMG/M) suite of tools managed by the JGI. The sequences were then biochemically characterized by a team led by Jennifer Doudna’s group at UC Berkeley.

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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 January 31, 2019 will be part of the next review.

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    MiddleGaylor Michael Beman UC Merced
    CSP New Investigator Call Ongoing
    The CSP New Investigator call targets investigators and research initiatives new to the JGI. Proposals submitted by March 2, 2020 will be part of the next review.

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    What Happens Underground Influences Global Nutrient Cycles
    Through the Facilities Integrating Collaborations for User Science (FICUS) program, the Environmental Molecular Sciences Laboratory (EMSL) and the DOE Joint Genome Institute (JGI) have selected 11 proposals for support from 53 received through a joint research call.

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    Characterizing Communities: Latest CSP Portfolio
    Through JGI's Community Science Program, 24 large-scale proposals have been accepted from 70 full submissions based on 92 letters of intent. Additionally, 40 percent of the proposals were submitted by researchers who had not been a primary investigator on any proposals previously accepted through JGI’s calls.

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    Learning to Look
    Using machine learning, JGI researchers combed through more than 70,000 microbial and metagenome datasets, ultimately identifying more than 10,000 inovirus-like sequences compared to the 56 previously known inovirus genomes.

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    Left to Right: Rex Malmstrom, Emiley Eloe-Fadrosh, and Simon Roux.
    JGI Early Career Researchers in mSystems Special Issue
    JGI researchers are among the authors who offer perspectives on what the next five years of innovation could look like. In one article, Rex Malmstrom and Emiley Eloe-Fadrosh outline more targeted approaches to reconstruct individual microbes in an environmental sample. In a separate article, Simon Roux makes a pitch for readers to get involved in the developing field of virus ecogenomics.

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Our Projects
Home › Our Projects › Approved User Proposals › Approved Proposals FY07

Approved Proposals FY07

Following are the approved user proposals for fiscal year 2007.

Community Science Program (CSP) Plans

Large Eukaryotes

Organism Proposer Affiliation
Aquilegia formosa Hodges UC Santa Barbara
Brachypodium distachyon (Poaceae) Vogel USDA-ARS
Gossypium (cotton) Paterson Univ. of Georgia
Manihot esculenta (cassava) Fauquet Danforth Plant Science Ctr.

Small Eukaryotes

Organism Proposer Affiliation
Cryphonectria parasitica (chestnut blight fungus) Nuss Univ. of Maryland Biotech. Inst.
Reef-building corals and dinoflagellate symbionts (ESTs from Acropora palmata, Montastraea faveolata, and Symbiodinium clade A and clade B) Medina Univ. of California, Merced
Fragilariopsis cylindrus (a diatom) Mock Univ. of Washington
Guillardia theta and Bigelowiella natans Archibald Dalhousie Univ.
Heterobasidion annosum
Stenlid Swedish Univ. of Agricultural Sciences
Three species of Neurospora (N. discreta, N. tetrasperma FGSC2508, N. tetrasperma FGSC2509)
Taylor Univ. of California, Berkeley
Peronosporomycete mtDNAs (26) Hudspeth Northern Illinois Univ.
Pleurotus ostreatus (oyster mushroom) Pisabarro Public Univ. of Navarre
Riftia pachyptila (deep-sea tubeworm) Girguis Harvard Univ.
Switchgrass Tobias USDA-ARS
Tetranychus urticae (two-spotted spider mite) Grbic Univ. of Western Ontario
Thellungiella halophila
Schumaker Univ. of Arizona
Mating loci from Volvox carteri and Chlamydomonas reinhardtii Umen Salk Inst.

Bacteria and Archaea

Organism Proposer Affiliation
Candidatus Amoebophilus asiaticus 5a2 and Encarsia symbiont Cand. Cardinium hertigii
Horn Univ. of Vienna
Actinobacteria (Arthrobacter chlorophenolicus A6 and Micrococcus luteus) Jansson Swedish Univ. of Agricultural Sciences
Beggiatoa alba Mueller Morgan State Univ.
Burkholderia (B. ambifaria IOP40-10, B. ambifaria MEX-5, B. graminis C4D1M, B. sp. SEMIA 6167, B. sp. strain H160, B. sp. strain 144F, B. sp. strain CCGE1001, B. sp. strain CCGE1003, B. cepacia ATCC 25416) Tiedje Michigan State Univ.
Anaerobic benzene-degrading methanogenic consortium (Chloroflexi, Desulfobacterium sp., Desulfosporosinus sp., Methanomicrobiales-like sp., Methanosaeta sp., Methanosarcinales-like spp) Edwards Univ. of Toronto
Crenothrix polyspora enrichment Wagner Univ. of Vienna
Cyanothece strains Pakrasi Washington Univ.
Dechlorinating community (KB-1) (Dehalococcoides, Geobacter, Methanosarcina, Spirochete, Sporomusa) Edwards Univ. of Toronto
Lithifying mat communities of marine stromatolites (Desulfovibrio sp. H0407_12.1Lac, Schizothrix gebeleni sp.A and sp. B, Solentia sp., Sulfate Reducing Bacterium sp. B, and sulfur-oxidizing bacteria) Decho Univ. of South Carolina
Candidatus Endomicrobium trichonymphae, Elusimicrobium minutum Pei191 Brune Max Planck Institute for Terrestrial Microbiology
Symbiont from the basal clade of the Frankiaceae Benson Univ. of Connecticut
Six freshwater iron-oxidizing bacteria (Gallionella ferruginea capsiferriformans ES-2, Leptothrix cholodnii SP-6, Rhodobacter sp. str. SW2, Rhodopseudomonas palustris TIE-1, and Sideroxydans lithotrophicus, Acidovorax delafieldii 2AN) Emerson Amer. Type Culture Collection
Microbiome resident in the foregut of the tammar wallaby (Macropus eugenii) McSweeney CSIRO
Methanomicrococcus blatticola Hackstein Radboud Univ. Nijmegen
Methylocella silvestris BL2, Methylocapsa acidiphila B2, and Beijerinckia indica subsp. indica Dunfield Inst. of Geological and Nuclear Sciences, New Zealand
Pedomicrobium manganicum Mackenzie, Univ. of Texas, Houston
Microbial community (plasmid mobilome) in wastewater treatment plant van der Meer Univ. of Lausanne
Rhizobium leguminosarum bv trifolii (strains WSM1325 and WSM2304) Reeve Murdoch Univ.
Near-shore anoxic basin: Saanich Inlet Hallam Univ. of British Columbia
Thauera sp. MZ1T Sayler Univ. of Tennessee
Thermolithobacter ferrireducens Wiegel Univ. of Georgia
Haloalkaliphilic sulfur-oxidizing bacteria (Thioalkalivibrio sp. HL-EbGR7, and T. sp. K90 mix) Muyzer Delft Univ. of Technology
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