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

News & Publications
Home › News Releases
Page 4 of 22« First«...23456...1020...»Last »

January 19, 2017

Seeking Structure With Metagenome Sequences

From sample to structure. Top: Researchers gathering samples from Great Boiling Spring in Nevada. Left: a snapshot of aligned metagenomic sequences. Each row is a different sequence (the different colors are the different amino acid groups). Each position (or column) is compared to all other positions to detect patterns of co-evolution. Bottom: the strength of the top co-evolving residues is shown as blue dots, these are also shown as colored lines on the structure above. The goal is to make a structure that makes as many of these contacts as possible. Right: a cartoon of the protein structure predicted. The protein domain shown is from Pfam DUF3794, this domain is part of a Spore coat assembly protein SafA. (Image of Great Boiling Spring by Brian Hedlund, UNLV. Protein structure and composite image by Sergey Ovchinnikov, UW)Metagenomics database helps fill in 10 percent of previously unknown protein structures For proteins, appearance matters. These important molecules largely form a cell’s structures and carry out its functions: proteins control growth and influence mobility, serve as catalysts, and transport or store other molecules. Comprised of long amino acid chains, the one-dimensional amino acid sequence… [Read More]

January 16, 2017

Tracking Antarctic Adaptations in Diatoms

Scanning electron micrograph of two cells of Fragilariopsis cylindrus. Shown are two silica shells (Frustules) in valve view. Magnification: 15,000X; scale bar: 5 μm (Image credit: Gerhard S. Dieckmann)Comparative genome analysis provides clues on how climate change might impact evolutionary adaptation limits Diatoms are a common type of photosynthetic microorganism, found in many environments from marine to soil; in the oceans, they are responsible for more than a third of the global ocean carbon captured during photosynthesis. This leads to a significant amount… [Read More]

January 10, 2017

Industrial Biotechnology Leader to Assume the Helm of the DOE Joint Genome Institute

Nigel MounceyAfter a 9-month national search, Nigel Mouncey, currently Research and Development Director for Bioengineering and Bioprocessing at Dow AgroSciences LLC, has been selected as the Director of the U.S. Department of Energy Joint Genome Institute (DOE JGI), a DOE Office of Science User Facility. “Nigel brings the perfect set of scientific and management skills as… [Read More]

November 17, 2016

Engineering a More Efficient System for Harnessing Carbon Dioxide

A MPI video featuring study senior author Tobias Erb discussing this project may be viewed at http://bit.ly/ErbCETCH.Despite the vast diversity of organisms on the planet that express enzymes for the conversion of carbon dioxide into such organic compounds as sugars – as plants do through photosynthesis – the efforts to harness these capabilities to transform CO2 into high-value products such as biofuel and renewable chemicals have met with limited success. While… [Read More]

November 2, 2016

2017 DOE Joint Genome Institute Community Science Program Allocations Announced

John Cushman of the University of Nevada seeks to establish the common or crystalline ice plant (Mesembryanthemum crystallinum L.) as a DOE JGI Flagship Genome species. (Image by Krzysztof Ziarnek, Kenraiz CC BY-SA 4.0 Wikipedia)Portfolio additions build upon contributions in sustainable biofuels, plant microbiomes and biogeochemistry. From deep within the Earth to the upper atmosphere, the organisms and ecosystems highlighted in the 37 projects selected for the 2017 Community Science Program (CSP) of the U.S. Department of Energy Joint Genome Institute (DOE JGI), a DOE Office of Science User… [Read More]

September 7, 2016

How Fungi Help Trees Tolerate Drought

The crosscut shows the fungal tissues - the fungal mantle around the root tip and the the fungal network of tendrils that penetrates the root of plants, or Hartig Net, between Pinus sylvestris plant root cells - in green. (Image by Maira de Freitas Pereira, INRA Nancy.)Genome of world’s most common fungal symbiont sheds light on drought resistance role The mutualistic relationship between tree roots and ectomycorrhizal (ECM) fungi has been shaping forest ecosystems since their inception. ECM fungi are key players supporting the growth, health and stress tolerance of forest trees globally, such as oak, pine, spruce, birch and beech,… [Read More]

September 6, 2016

10 New Projects to be Supported Under Joint DOE User Facility Initiative

This diagram from Petr Baldrian’s proposal shows the seasonal differences in the carbon cycle processes in the temperate and boreal coniferous forests. During vegetation seasons, depicted by September on the left, photosynthesis products are allocated to soil via tree roots. When photosynthesis stops in winter, depicted by March on the right, decomposition is the most important carbon cycle process. (Image courtesy of Petr Baldrian)The U.S. Department of Energy Joint Genome Institute (DOE JGI) and the Environmental Molecular Sciences Laboratory (EMSL) have accepted 10 projects submitted during the 2017 call for proposals for their joint “Facilities Integrating Collaborations for User Science” (FICUS) initiative. These new research projects all involve collaboration between two user facilities that are stewarded by the DOE Office… [Read More]

August 17, 2016

Unveiled: Earth’s Viral Diversity

virome-graphic_art-by-Z-Rostomian-LBNLEnvironmental datasets help researchers double the number of microbial phyla known to be infected by viruses. The number of microbes in, on, and around the planet – on the order of a nonillion, or 1030 – is estimated to outnumber the stars in the Milky Way. Microbes are known to play crucial roles in regulating… [Read More]

August 15, 2016

Expanding the Stable of Workhorse Yeasts

One of the genomes sequenced for this study was of the yeast Scheffersomyces stipitis. (Courtesy of Tom Jeffries, University of Wisconsin-Madison)New genome sequences target next generation of yeasts with improved biotech uses The yeast Saccharomyces cerevisiae was a part of human civilization before history was recorded. It is essential for making bread, beer and wine, and it is ubiquitous. It is not, however, typical of the more than 1,500 yeast species found around the world…. [Read More]

July 19, 2016

Comparing Fungal Secretions to Uncover Carbon Compound Degradation Pathways

Pyrenochaeta sp. DS3sAY3a growing in liquid culture. As the fungus grows, brown-colored manganese oxides are formed. Here, the oxides can be seen associated with biomass and suspended in solution. (Carolyn Zeiner)Their unassuming appearances may cause them to be overshadowed by the plants or animals in their natural habitats, but fungi play key roles in maintaining their ecosystems. From breaking down leaf litter and decaying wood in forests to cleaning contaminated soils and waters, fungal enzymes are being characterized for potential use in a wide variety… [Read More]
Page 4 of 22« First«...23456...1020...»Last »

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