DOE Joint Genome Institute

  • COVID-19
  • About Us
  • Contact Us
  • Our Science
    • DOE Mission Areas
    • Science Programs
    • Science Highlights
    • Scientists
    A vertical tree stump outdoors with about a dozen shiitake mushrooms sprouting from its surface.
    Tracing the Evolution of Shiitake Mushrooms
    Understanding Lentinula genomes and their evolution could provide strategies for converting plant waste into sugars for biofuel production. Additionally, these fungi play a role in the global carbon cycle.

    More

    Soil Virus Offers Insight into Maintaining Microorganisms
    Through a collaborative effort, researchers have identified a protein in soil viruses that may promote soil health.

    More

    Data yielded from RIViT-seq increased the number of sigma factor-gene pairs confirmed in Streptomyces coelicolor from 209 to 399. Here, grey arrows denote previously known regulation and red arrows are regulation identified by RIViT-seq; orange nodes mark sigma factors while gray nodes mark other genes. (Otani, H., Mouncey, N.J. Nat Commun 13, 3502 (2022). https://doi.org/10.1038/s41467-022-31191-w)
    Streamlining Regulon Identification in Bacteria
    Regulons are a group of genes that can be turned on or off by the same regulatory protein. RIViT-seq technology could speed up associating transcription factors with their target genes.

    More

  • Our Projects
    • Search JGI Projects
    • DOE Metrics/Statistics
    • Approved User Proposals
    • Legacy Projects
    The switchgrass diversity panel growing at the Kellogg Biological Station in Michigan. (David Lowry)
    Mapping Switchgrass Traits with Common Gardens
    The combination of field data and genetic information has allowed researchers to associate climate adaptations with switchgrass biology.

    More

    Artist rendering of genome standards being applied to deciphering the extensive diversity of viruses. (Illustration by Leah Pantea)
    Expanding Metagenomics to Capture Viral Diversity
    Along with highlighting the viruses in a given sample, metagenomics shed light on another key aspect of viruses in the environment — their sheer genetic diversity.

    More

    Photograph of a stream of diatoms beneath Arctic sea ice.
    Polar Phytoplankton Need Zinc to Cope with the Cold
    As part of a long-term collaboration with the JGI Algal Program, researchers studying function and activity of phytoplankton genes in polar waters have found that these algae rely on dissolved zinc to photosynthesize.

    More

  • Data & Tools
    • IMG
    • Data Portal
    • MycoCosm
    • PhycoCosm
    • Phytozome
    • GOLD
    Abstract image of gold lights and squares against a black backdrop
    Silver Age of GOLD Introduces New Features
    The Genomes OnLine Database makes curated microbiome metadata that follows community standards freely available and enables large-scale comparative genomics analysis initiatives.

    More

    Graphical overview of the RNA Virus MetaTranscriptomes Project. (Courtesy of Simon Roux)
    A Better Way to Find RNA Virus Needles in the Proverbial Database Haystacks
    Researchers combed through more than 5,000 data sets of RNA sequences generated from diverse environmental samples around the world, resulting in a five-fold increase of RNA virus diversity.

    More

    HPCwire Editor's Choice Award (logo crop) for Best Use of HPC in the Life Sciences
    JGI Part of Berkeley Lab Team Awarded Best Use of HPC in Life Sciences
    The HPCwire Editors Choice Award for Best Use of HPC in Life Sciences went to the Berkeley Lab team comprised of JGI and ExaBiome Project team, supported by the DOE Exascale Computing Project for MetaHipMer, an end-to-end genome assembler that supports “an unprecedented assembly of environmental microbiomes.”

    More

  • User Programs
    • Calls for Proposals
    • Special Initiatives & Programs
    • Product Offerings
    • User Support
    • Policies
    • Submit a Proposal
    Digital ID card with six headshots reads: Congratulations to our 2022 Function Genomics recipients!
    Final Round of 2022 CSP Functional Genomics Awardees
    Meet the final six researchers whose proposals were selected for the 2022 Community Science Program Functional Genomics call.

    More

    CSP New Investigators FY23 R1
    JGI Announces First Round of 2023 New Investigator Awardees
    Twice each year we look for novel research projects aligned with DOE missions and from PIs who have not led any previously-accepted proposals through the CSP New Investigator call.

    More

    screencap from Amundson and Wilkins subsurface microbiome video
    Digging into Microbial Ecosystems Deep Underground
    JGI users and microbiome researchers at Colorado State University have many questions about the microbial communities deep underground, including the role viral infection may play in other natural ecosystems.

    Read more

  • News & Publications
    • News
    • Blog
    • Podcasts
    • Webinars
    • Publications
    • Newsletter
    • Logos and Templates
    • Photos
    2022 JGI-UC Merced interns (Thor Swift/Berkeley Lab)
    Exploring Possibilities: 2022 JGI-UC Merced Interns
    The 2022 UC Merced intern cohort share how their summer internship experiences have influenced their careers in science.

    More

    Using Team Science to Build Communities Around Data
    As the data portals grow and evolve, the research communities further expand around them. But with two projects, communities are forming to generate high quality genomes to benefit researchers.

    More

    Cow Rumen and the Early Days of Metagenomics
    Tracing a cow rumen dataset from the lab to material for a hands-on undergraduate research course at CSU-San Marcos that has since expanded into three other universities.

    More

News & Publications
Home › News Releases › The DOE Joint Genome Institute Expands Capabilities via New Partnerships

May 15, 2013

The DOE Joint Genome Institute Expands Capabilities via New Partnerships

With the publication last year of its strategic plan, “Forging the Future — A Ten-Year Strategic Vision” the U.S. Department of Energy Joint Genome Institute (DOE JGI) has positioned itself to provide the most current technology and expertise to their users so that they can address pressing energy and environmental scientific challenges.

An important early step in this process is the launch of the Emerging Technologies Opportunity Program (ETOP). The primary purpose of the ETOP is to develop and support selected new technologies that DOE JGI could establish to add value to the high throughput sequencing it currently carries out for its users. The program was one of several recommendations that emerged from the DOE JGI’s strategic planning as well as a complementary process carried out by DOE’s Office of Biological and Environmental Research. Now, a new set of partnerships is taking shape in response to the ETOP’s first call for proposals. These span the development of new scalable DNA synthesis technologies to the latest approaches to high throughput sequencing and characterization of single microbial cells from complex environmental samples.

Photo: One of the challenges to be addressed via the ETOP effort relates to the assignment of genome fragments (represented by dots) to genomes (represented by clusters of colored dots, separated from adjacent clusters by dark barriers). Here a subset of data from a complex sample was analyzed. Sequence compositional information was used to generate clusters in an emergent self organizing map (ESOM). (B. Thomas and J. Banfield)

Photo: One of the challenges to be addressed via the ETOP effort relates to the assignment of genome fragments (represented by dots) to genomes (represented by clusters of colored dots, separated from adjacent clusters by dark barriers). Here a subset of data from a complex sample was analyzed. Sequence compositional information was used to generate clusters in an emergent self organizing map (ESOM). (B. Thomas and J. Banfield)

“A core philosophy of the DOE JGI is that our suite of technical and analytical capabilities needs to evolve continuously so that the scientific achievements of our users can be maximized,” said Jim Bristow, who oversees the ETOP as DOE JGI’s Deputy Director of Science Programs.  “This occurs by building new scientific capabilities at the DOE JGI itself, and by enlisting partners, like the ones we’ve identified through this program, to develop and deploy highly-specialized technologies that complement activities at our Walnut Creek facility.  While state-of-the art massive-scale sequencing remains a critical component of the DOE JGI, other large-scale capabilities particularly those that will help link sequence to function will be provided to JGI users in the future,” Bristow said.

When the DOE JGI was founded back in 1997 to help accelerate the Human Genome Project (HGP) effort, the partnership consisted of DOE National Laboratory and university partners.  After completing the DOE’s commitment to the HGP in 2004, the DOE JGI opened its doors as a national user facility advancing the frontiers of genomics for energy and environmental applications.  In 2012 alone, the Institute completed over 2,600 projects.

Photo: Microfluidic device involved in high-throughput sorting of microbial cells. (Roman Stocker)

Photo: Microfluidic device involved in high-throughput sorting of microbial cells. (Roman Stocker)

For the first cycle of the ETOP, the DOE JGI has selected these six new partnerships:

  • “Single cell approaches to metagenomics,” proposed by Stephen Quake of Stanford University. This technology could make it easier to isolate single cells of interest from complex environmental samples.
  • “Accurate gene synthesis with tag-directed retrieval of sequence-verified DNA molecules,” proposed by Jay Shendure of the University of Washington. This technology could streamline the DNA synthesis pipeline and increase the output.
  • “High-throughput sorting of microbial cells with specific functional traits for single cell genomics by combining labeling with heavy water, Raman microspectroscopy, microfluidics and flow cytometry,” proposed by Roman Stocker of MIT and Michael Wagner of the University of Vienna (Austria). This technology could accelerate the functional characterization of genes from metagenomic sequencing experiments, one of DOE JGI’s highest priorities.
  • “Generation of high-quality genomic DNA from plants and other organisms, large insert libraries and high-quality physical maps for improved physical map and sequence level-assemblies,” proposed by Rod Wing of the Arizona Genomics Institute (AGI). This technology could make considerably easier the isolation of DNA from plants in amounts and quality that can be more effectively sequenced by the DOE JGI.
  • “Development of a pipeline for high-throughput recovery of near-complete and complete microbial genomes from complex metagenomic datasets,” proposed by Jill Banfield of the University of California, Berkeley and Lawrence Berkeley National Laboratory, Chongle Pan of Oak Ridge National Laboratory, and Brian Thomas of the University of California, Berkeley. This technology could result in better methods for isolating and characterizing entire microbial genomes from the fragmentary sequences typical of environmental samples.
  • “Development and Implementation of High Throughput Methods for Fungal Culturing and Nucleic Acid Isolation,” proposed by Jon Magnuson of Pacific Northwest National Laboratory. Similar to the AGI proposal above, this technology could make the isolation of DNA from fungi in amounts and quality that can be more effectively sequenced by DOE JGI considerably easier.

The DOE JGI expects to commit approximately $3.5 million over the next two years to the new ETOP initiatives.

“The DOE JGI strives to integrate these expanded activities in innovative and effective ways,” said Bristow.  “This is critical if the biological sciences are to realize the full benefits and promise of genome sequencing.”

 

Share this:

  • Click to share on Facebook (Opens in new window)
  • Click to share on LinkedIn (Opens in new window)
  • Click to share on Pinterest (Opens in new window)
  • Click to share on Twitter (Opens in new window)
  • Click to print (Opens in new window)

The U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility at Lawrence Berkeley National Laboratory, is committed to advancing genomics in support of DOE missions related to clean energy generation and environmental characterization and cleanup. JGI provides integrated high-throughput sequencing and computational analysis that enable systems-based scientific approaches to these challenges. Follow @jgi on Twitter.

DOE’s Office of Science is the largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time. For more information, please visit science.energy.gov.

Filed Under: News Releases

More topics:

  • COVID-19 Status
  • News
  • Science Highlights
  • Blog
  • Webinars
  • CSP Plans
  • Featured Profiles

Related Content:

Supercharging SIP in the Fungal Hyphosphere

Green plant matter grows from the top, with the area just beneath the surface also visible as soil, root systems and a fuzzy white substance surrounding them.

New Research Sheds Light on Diversity in the Deep Sea

A photo taken in the deep sea. Black clouds billow out of hydrothermal vents.

Sequencing Sphagnum Leads to Discovery of Sex Chromosomes

A photo of two sphagnum species: S. divinum (red) and S. angustifolium (green)]

Busting the Unbreakable Lignin

Pictured is a micrograph of Neocallimastix californiae.

Tracing the Evolution of Shiitake Mushrooms

A vertical tree stump outdoors with about a dozen shiitake mushrooms sprouting from its surface.

JGI announces final round of 2022 Functional Genomics awardees

Digital ID card with six headshots reads: Congratulations to our 2022 Function Genomics recipients!
  • Careers
  • Contact Us
  • Events
  • User Meeting
  • MGM Workshops
  • Internal
  • Disclaimer
  • Credits
  • Policies
  • Emergency Info
  • Accessibility / Section 508 Statement
  • Flickr
  • LinkedIn
  • RSS
  • 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

© 1997-2023 The Regents of the University of California