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 FY16

Approved Proposals FY16

Following are the approved user proposals for fiscal year 2016 including CSP, CSP Small-Scale, Synthesis, and FICUS projects.

FY 2016 Community Science Program (CSP) Plans

PI Affiliation Project Description
Catcheside, David Flinders University (Australia) Acquisition of the sequestrate (truffle like) habit by basidiomycete macrofungi
Cooper, Elizabeth Clemson University Comparative transcriptomics of sweet and grain sorghum to understand the mechanism and timing of sugar accumulation in an important bioenergy crop
de Vries, Ronald CBS-KNAW Fungal Biodiversity Centre (Netherlands) Dissecting the different approaches of ascomycete fungi to degrade plant biomass
DeLong, Ed University of Hawaii at Manoa Going long and going deep: Comprehensive open ocean community single cell genome sequencing at the model open ocean time series study site, station ALOHA
Dollhofer, Veronika Bavarian State Research Center for Agriculture (Germany) Anaerobic fungi and assessment of their potential for biogas production
Duplessis, Sebastien INRA (France) Sequencing a reference genome for Phakopsora pachyrhizi, the fungal pathogen responsible for the Asian Soybean Rust
Francis, Christopher Stanford University Metagenomic characterization of nitrogen-cycling microbial communities impacting uranium release in the Upper Colorado River Basin
Hamelin, Richard University of British Columbia (Canada) Pathobiome of bioenergy trees
Hibbett, David Clark University Comparative and functional genomics of shiitake mushrooms: an international collaboration to resolve evolutionary relationships, substrate specificity, growth profiles, and routes to domestication in the amphi-Pacific genus Lentinula
Juenger, Tom University of Texas at Austin Exploring natural genetic diversity in switchgrass (Panicum virgatum) and its microbiome
Kalyuzhnaya, Marina University of Washington Systems level insights into methane cycling in arid and semi-arid ecosystems via community metagenomics and metatranscriptomics
Lorito, Matteo University of Naples (Italy) Supporting the development of microbial probiotics for grasses useful in sustainable bioenergy production
Martin, Francis INRA (France) 1KFG: Deep sequencing of ecologically-relevant Dikarya
Mayali, Xavier Lawrence Livermore National Laboratory Influence of phycosphere-associated bacteria on microalgal biofuel production
McMahon, Katherine University of Wisconsin-Madison Diel cycles of gene expression in oligotrophic, dystrophic, and eutrophic lakes to identify new gene functions and dissect carbon cycling metabolisms
Merchant, Sabeeha University of California, Los Angeles Comparative genomics and expression profiling of snow algae Chlamydomonas cribrum and Chloromonas nivalis
Niyogi, Kris University of California, Berkeley Functional genomics of photosynthesis in Chlamydomonas, JGI’s flagship alga
O’Malley, Michelle University of California, Santa Barbara Genomic basis for syntrophic interactions between anaerobic gut fungi and methanogenic archaea
Pires, J. Chris University of Missouri-Columbia Investigating the diversity of mycorrhizal fungi to understand the evolution and function of symbiosis with orchids
Plett, Jonathan University of Western Sydney (Australia) Exploring the genomic basis for the global diversification by the ectomycorrhizal genus Pisolithus
Poland, Jesse Kansas State University The Intermediate Wheatgrass Genome: A resource for understanding mechanisms of perenniality and accelerating the development of perennial crops
Rappe, Michael University of Hawaii at Manoa Metagenomics of viral and microbial communities inhabiting warm, anoxic fluids of the sediment-buried deep ocean crust
Schachtman, Daniel University of Nebraska Systems analysis of the physiological and molecular mechanisms of Sorghum nitrogen use efficiency, water use efficiency and interactions with the soil microbiome
Spatafora, Joey Oregon State University Genomics of the early diverging lineages of fungi and their transition to terrestrial, plant-based ecologies
Umen, James Donald Danforth Plant Science Center Single cell and population dynamics of chromatin across the diurnal cycle in the model alga Chlamydomonas
Walsh, David Concordia University (Canada) Microbial metagenomics of carbon cycling communities in northern aquatic ecosystems
Wrighton, Kelly Ohio State University Life in the extreme deep terrestrial subsurface: microbial metabolism before and after shale gas extraction

Small-Scale Proposals

Proposer Affiliation Project Description
Beman, J Michael University of California, Merced Metagenomics of methane production and oxidation in high altitude lakes of Yosemite National Park
Chistoserdova, Ludmila University of Washington Understanding methane cycling through manipulation of synthetic methane-oxidizing communities
Cullings, Ken NASA Ames Extreme endosymbiosis: An investigation into a unique fungal microbiome found in geothermal ecosystems in Yellowstone National Park and New Zealand
DeAngelis, Kristen University of Massachusetts, Amherst Expanding genomic diversity of terrestrial bacteria: linking genes to metabolism in the slower-growing members of forest soil bacterial communities
Kostka, Joel Georgia Institute of Technology The role of the Sphagnum microbiome in carbon and nutrient cycling in peatlands
McMahon, Katherine University of Wisconsin-Madison Reference genomes for abundant freshwater taxa – Actinobacteria and Verrucomicrobia phase 2
Meredith, Laura Stanford University Microbial, chemical, and physical drivers of COS fluxes and 18O-CO2 exchange rates in soils
Miller, Christopher University of Colorado, Denver Developing a systems-level understanding of biotic and abiotic controls on microbial methane cycling in freshwater wetlands
Redmond, Molly University of North Carolina, Charlotte Metagenomic sequencing of methane-oxidizing mesocosms from the Gulf of Mexico and Hudson Canyon
Rich, Jeremy Brown University Metagenomic sequencing of an uncultivated bacterial phylum in marine sediments amended with organic carbon and nitrate
Saito, Mak Woods Hole Oceanographic Institution Characterizing Synechococcus dominated populations from the Costa Rica dome and surrounding waters
Shade, Ashley Michigan State University Response and recovery of surface soil microbial communities to an ongoing underground coalmine fire
Simister, Rachel University of British Columbia Linking microbial genomic capacity to geochemical process in the deep terrestrial biosphere
Slonczewski, Joan Kenyon College Cyanobacterial communities of Antarctic Lake Fryxell liftoff mats and glacier meltwater
Tolar, Bradley Stanford University Monitoring the transcriptional response of a representative low-salinity ammonia-oxidizing thaumarchaeote to shifts in environmental conditions
Walsh, Davi Concordia University Metagenomics of western Arctic Ocean microbial communities
Wilkins, Michael Ohio State University Seasonal sulfur cycling as a control on methane flux in carbon-rich prairie pothole sediment ecosystems
Wrighton, Kelly Ohio State University Identifying key genomes and metabolisms responsible for near-surface methane cycling in freshwater wetlands

Synthesis Proposals

Proposer Affiliation Project Description
Chang, Jui-Jen Biodiversity Research Center,Academia Sinica Designer Operons-A biomimic approach to the regulation of an enzyme cocktail for an artificial enzyme complex
Chen, Brandon Genomatica, Inc. Engineering efficient methanol utilization for renewable chemicals
McCourt, Peter University of Toronto Exploring the perception landscape of the strigolactone receptor
Prather, Kristala Massachusetts Institute of Technology Combinatorial assembly, screening and functional characterization of a recombinant glucaric acid pathway in S. cerevisiae
Shen, Ben The Scripps Research institute Construction of bacterial artificial chromosome (BAC) vector libraries for comparative genomics, elucidation of gene functions and heterologous expression of targeted genes
Smanski, Mike University of Minnesota Towards a mechanistic understanding of disease suppressive soils: Refactoring natural product gene clusters
Wang, Clay University of Southern California Identification of fungal secondary metabolites with novel structures
Zimmer, Jochen University of Virginia Synthesis of cellulose synthase genes implicated in primary and secondary plant cell wall formation for structural and functional analyses of plant cellulose biosynthesis

FY 2016 Facilities Integrating Collaboration for User Science (FICUS) JGI-EMSL Plans

Proposer Affiliation Project Description
Bell-Pedersen, Deborah Texas A&M University Specialized Ribosomes: A New Frontier in Gene Regulation
Cardon, Zoe Marine Biological Laboratory 3D Reality Check: Developing Structural Support for Predicting Microbial Function and Interpreting Microbial “Omics” Data
Doty, Sharon University of Washington Nitrogen fixation in Populus: Identification and localization of the key diazotrophs in planta
Duhaime, Melissa University of Michigan Building the phage-host-environment interaction data to scale from genes-to-ecosystems: Towards predictive modeling of wild microbial and viral community dynamics
Eastwood, Dan Swansea University (UK) Genomes to dynamic decay communities: Understanding fungal interactions during early decomposition events in natural lignocellulosic substrate
Neumann, Rebecca University of Washington A Rhizosphere-Scale Investigation of the Relationship Between Plant Productivity and Methane Emissions from Wetlands
Orphan, Victoria California Institute of Technology Fluorescence-based cell sorting and targeted proteomic analysis of active methane-oxidizing syntrophic consortia from environmental samples
Pan, Chongle Oak Ridge National Laboratory Integrated Omics Analyses of a Populus Pedigree for Crop Improvement
  • 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