DOE Joint Genome Institute

  • About Us
  • Phone Book
  • Contact Us
  • Our Science
    • DOE Mission Areas
    • Bioenergy Research Centers
    • Science Programs
    • Products
    • Science Highlights
    • Scientists
    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.

    Read more

    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.

    Read more

    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.

    Read more

  • Our Projects
    • Search JGI Projects
    • DOE Metrics/Statistics
    • Approved User Proposals
    • Legacy Projects
    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.

    Read more

    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.

    Read more

    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.

    Read more

  • Data & Tools
    • IMG
    • Genome Portal
    • MycoCosm
    • Phytozome
    • GOLD
    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).

    Read more

    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.

    Read more

    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.

    Read more

  • User Programs
    • Calls for User Proposals
    • Special Initiatives & Programs
    • User Support
    • Submit a Proposal
    martin-adams-unsplash
    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.

    Read more

    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.

    Read more

    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.

    Read more

  • News & Publications
    • News Releases
    • Blog
    • Publications
    • Scientific Posters
    • Newsletter
    • Logos
    • Photos
    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.

    Read more

    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.

    Read more

    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.

    Read more

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.
  • Approved Proposals FY20
  • Approved Proposals FY19
  • Approved Proposals FY18
  • Approved Proposals FY17
  • Approved Proposals FY16
  • Approved Proposals FY15
  • Approved Proposals FY14
  • Approved Proposals FY13
  • Approved Proposals FY12
  • Approved Proposals FY11
  • Approved Proposals FY10
  • Approved Proposals FY09
  • Approved Proposals FY08
  • Approved Proposals FY07
  • Approved Proposals FY06
  • Approved Proposals FY05
  • ETOP Projects

More topics:

  • News Releases
  • Science Highlights
  • Blog
  • CSP Plans
  • Featured Profiles
  • Careers
  • Contact Us
  • Events
  • User Meeting
  • MGM Workshops
  • Internal
  • Disclaimer
  • Credits
  • Emergency Info
  • Accessibility / Section 508 Statement
  • RSS feed
  • Facebook
  • Flickr
  • Instagram
  • LinkedIn
  • Twitter
  • YouTube
Lawrence Berkeley National Lab Biosciences Area
A project of the US Department of Energy, Office of Science

JGI is a DOE Office of Science User Facility managed by Lawrence Berkeley National Laboratory

© 1997-2019 The Regents of the University of California