DOE Joint Genome Institute

  • COVID-19
  • About Us
  • Contact Us
  • Our Science
    • DOE Mission Areas
    • Bioenergy Research Centers
    • Science Programs
    • Science Highlights
    • Scientists
    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

    (PXFuel)
    Designer DNA: JGI Helps Users Blaze New Biosynthetic Pathways
    In a special issue of the journal Synthetic Biology, JGI scientific users share how they’ve worked with the JGI DNA Synthesis Science Program and what they’ve discovered through their collaborations.

    More

    A genetic element that generates targeted mutations, called diversity-generating retroelements (DGRs), are found in viruses, as well as bacteria and archaea. Most DGRs found in viruses appear to be in their tail fibers. These tail fibers – signified in the cartoon by the blue virus’ downward pointing ‘arms’— allow the virus to attach to one cell type (red), but not the other (purple). DGRs mutate these ‘arms,’ giving the virus opportunities to switch to different prey, like the purple cell. (Courtesy of Blair Paul)
    A Natural Mechanism Can Turbocharge Viral Evolution
    A team has discovered that diversity generating retroelements (DGRs) are not only widespread, but also surprisingly active. In viruses, DGRs appear to generate diversity quickly, allowing these viruses to target new microbial prey.

    More

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

    This data image shows the monthly average sea surface temperature for May 2015. Between 2013 and 2016, a large mass of unusually warm ocean water--nicknamed the blob--dominated the North Pacific, indicated here by red, pink, and yellow colors signifying temperatures as much as three degrees Celsius (five degrees Fahrenheit) higher than average. Data are from the NASA Multi-scale Ultra-high Resolution Sea Surface Temperature (MUR SST) Analysis product. (Courtesy NASA Physical Oceanography Distributed Active Archive Center)
    When “The Blob” Made It Hotter Under the Water
    Researchers tracked the impact of a large-scale heatwave event in the ocean known as “The Blob” as part of an approved proposal through the Community Science Program.

    More

    A plantation of poplar trees. (David Gilbert)
    Genome Insider podcast: THE Bioenergy Tree
    The US Department of Energy’s favorite tree is poplar. In this episode, hear from ORNL scientists who have uncovered remarkable genetic secrets that bring us closer to making poplar an economical and sustainable source of energy and materials.

    More

  • Data & Tools
    • IMG
    • Data Portal
    • MycoCosm
    • PhycoCosm
    • Phytozome
    • GOLD
    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

    With a common set of "baseline metadata," JGI users can more easily access public data sets. (Steve Wilson)
    A User-Centered Approach to Accessing JGI Data
    Reflecting a structural shift in data access, the JGI Data Portal offers a way for users to more easily access public data sets through a common set of metadata.

    More

    Phytozome portal collage
    A More Intuitive Phytozome Interface
    Phytozome v13 now hosts upwards of 250 plant genomes and provides users with the genome browsers, gene pages, search, BLAST and BioMart data warehouse interfaces they have come to rely on, with a more intuitive interface.

    More

  • User Programs
    • Calls for Proposals
    • Special Initiatives & Programs
    • Product Offerings
    • User Support
    • Policies
    • Submit a Proposal
    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

    Yeast strains engineered for the biochemical conversion of glucose to value-added products are limited in chemical output due to growth and viability constraints. Cell extracts provide an alternative format for chemical synthesis in the absence of cell growth by isolating the soluble components of lysed cells. By separating the production of enzymes (during growth) and the biochemical production process (in cell-free reactions), this framework enables biosynthesis of diverse chemical products at volumetric productivities greater than the source strains. (Blake Rasor)
    Boosting Small Molecule Production in Super “Soup”
    Researchers supported through the Emerging Technologies Opportunity Program describe a two-pronged approach that starts with engineered yeast cells but then moves out of the cell structure into a cell-free system.

    More

    These bright green spots are fluorescently labelled bacteria from soil collected from the surface of plant roots. For reference, the scale bar at bottom right is 10 micrometers long. (Rhona Stuart)
    A Powerful Technique to Study Microbes, Now Easier
    In JGI's Genome Insider podcast: LLNL biologist Jennifer Pett-Ridge collaborated with JGI scientists through the Emerging Technologies Opportunity Program to semi-automate experiments that measure microbial activity in soil.

    More

  • News & Publications
    • News
    • Blog
    • Podcasts
    • Webinars
    • Publications
    • Newsletter
    • Logos and Templates
    • Photos
    A view of the mangroves from which the giant bacteria were sampled in Guadeloupe. (Hugo Bret)
    Giant Bacteria Found in Guadeloupe Mangroves Challenge Traditional Concepts
    Harnessing JGI and Berkeley Lab resources, researchers characterized a giant - 5,000 times bigger than most bacteria - filamentous bacterium discovered in the Caribbean mangroves.

    More

    In their approved proposal, Frederick Colwell of Oregon State University and colleagues are interested in the microbial communities that live on Alaska’s glacially dominated Copper River Delta. They’re looking at how the microbes in these high latitude wetlands, such as the Copper River Delta wetland pond shown here, cycle carbon. (Courtesy of Rick Colwell)
    Monitoring Inter-Organism Interactions Within Ecosystems
    Many of the proposals approved through JGI's annual Community Science Program call focus on harnessing genomics to developing sustainable resources for biofuels and bioproducts.

    More

    Coloring the water, the algae Phaeocystis blooms off the side of the sampling vessel, Polarstern, in the temperate region of the North Atlantic. (Katrin Schmidt)
    Climate Change Threatens Base of Polar Oceans’ Bountiful Food Webs
    As warm-adapted microbes edge polewards, they’d oust resident tiny algae. It's a trend that threatens to destabilize the delicate marine food web and change the oceans as we know them.

    More

News & Publications
Home › News Releases › Bigger is Better: DOE JGI Announces 2011 Community Sequencing Program Portfolio

October 4, 2010

Bigger is Better: DOE JGI Announces 2011 Community Sequencing Program Portfolio

The U.S. Department of Energy (DOE) Joint Genome Institute (JGI) has selected 35 new genomic sequencing projects for its 2011 Community Sequencing Program (CSP)—a targeted sampling of the planet’s biodiversity—to be characterized for bioenergy and environmental applications.

Supported by the Office of Biological and Environmental Research in the DOE Office of Science, the DOE JGI’s Community Sequencing Program enables scientists from universities and national laboratories around the world to probe the hidden world of microbes and plants for innovative solutions to the nation’s major challenges in energy, climate, and environment. This year’s portfolio is composed mostly of large-scale projects, which DOE JGI Director Eddy Rubin said was in keeping with the facility’s mission of large-scale genomics and analysis, and that meet the DOE missions of bioenergy, carbon cycling and biogeochemistry.

“Advances in sequencing technologies are really changing the landscape and have dramatically increased data output,” he said. “This has led to enormous changes which have impacted the science we produce. In the past year alone, the JGI’s sequence output has increased fivefold to five terabytes or five trillion nucleotides. Connected with the increased productivity, we’re beginning to position the JGI to work on projects of tera- and peta- or quadrillion-base scale. Our mission hasn’t changed; what is changing is the scale and complexity of the projects – which will increase. This highlights one of the directions genomics is going as data output begins to rival the output of the high-energy physics and astronomy communities.”

To highlight the directional shift, the CSP 2011 call urged researchers to submit proposals for projects that advance capabilities in fields such as large-scale resequencing, single-cell genomics and metatranscriptomics.

A total of 35 proposals were approved from the 127 submitted, selected from the 145 letters of intent originally received. Of the approved proposals, two involve plant genomes and two involve algal genomes; 10 are fungal projects; nine are microbial projects, six of which involve single-cell genomics; and 12 are metagenome (microbial communities) or metatranscriptome projects. The projects approved by an outside review panel and vetted by the DOE make the most of the DOE JGI’s increased sequencing capacity, allocating 10 trillion bases (TB or terabases), a 30-fold increase compared with last year’s one-third of a trillion nucleotides.

One of the microbial projects approved builds upon a previous CSP project to realize the evolutionary diversity of bacteria and archaea in nature. Since its inception, more than 100 microbes have been sequenced as part of the Genome Encyclopedia of Bacteria and Archaea (GEBA) to provide information on unrepresented branches of the Tree of Life. An analysis of the first 56 genomes from the GEBA project was published in the December 24, 2009 edition of the journal Nature. Now the team, led by the DOE JGI and UC Davis researcher Jonathan Eisen, plans to sequence another 61 bacteria and archaea not just to increase the phylogenetic reference genomes but to also identify new proteins and subfamilies that could be useful to the DOE missions.

The single largest project, and the Institute’s largest to date, involves sequencing barley, which has an anticipated five-billion base genome. Proposed by Gary Muehlbauer of the University of Minnesota, barley ranks fifth in the world among all crops cultivated and is grown on four million acres in the United States alone. The crop can be used to produce ethanol from the grain or for cellulosic ethanol from the straw.

One of the projects approved for CSP 2011 involves resequencing the wild grass Brachypodium distachyon. Resequencing, as the name suggests, revisits previously sequenced genomes but focuses on comparing new data with a reference model. Earlier this year, the genome sequence of this plant was published in the journal Nature to help researchers develop grasses tailored to serve as feedstocks for biofuel production. Led by John Vogel of the US Department of Agriculture Agricultural Research Service, the project involves sequencing 50 inbred lines of the grass to further develop genomic resources for Brachypodium and carry out comparisons of their gene sets to enable identification of candidate genes involved in traits such as drought tolerance that are of interest to the DOE.

Researchers at the DOE JGI have been among the pioneers of the methodology known as single-cell genomics in which the DNA isolated from a lone cell is amplified allowing researchers to study organisms that have not or cannot be cultured in a laboratory setting. This is a critically important capability as it is well known among microbiologists that 99 percent of the microbial world is difficult to grow in culture and thus very difficult to study. Two-thirds of the approved CSP 2011 microbial projects involve the use of single cell genomics to learn more about uncultured microbes found in ecosystems such as deep-sea hydrothermal vents and terrestrial subsurface aquifers.

For example, Stefan Sievert from the Woods Hole Oceanographic Institute is interested in using single-cell genomics to sequence nearly a dozen genomes of uncultivated bacteria that are found in deep-sea hydrothermal vents to learn about their roles in the global carbon, sulfur and nitrogen cycles. Additionally, the genomic information could be used to reduce sulfur emissions and resulting smog and acid rain.

Another project that involves the application of single cell genomics focuses on the microbial diversity in the methane-rich environment of western Greece’s Etoliko lagoon, which essentially supports two ecosystems by having both an oxygen-rich area and a distinct oxygen-poor zone. The anoxic zone is noted for having increased levels of sulfides and salinity. Led by George Tsiamis of Greece’s University of Ioannina, the proposal calls for sequencing nearly two-dozen microbes to learn more about the microbial diversity in the lagoon, and the genomic information collected will also enrich the DOE JGI’s ongoing GEBA project.

Metatranscriptomics focuses on the complex region of the complete genetic code that is transcribed into RNA molecules and provides information on gene expression and gene function. Half of the projects that look at the genomes of microbial communities (metagenomes) also involve plans to study their transcriptomes.

One of the algal projects is noteworthy partly due to the stated intent of involving student participation to boost undergraduate education in genomics and informatics. A team including DOE JGI’s Education head Cheryl Kerfeld, who was recently honored by the American Society for Biochemistry and Molecular Biology, plans to study algal strains from isolated acidic waters to understand their role in the carbon cycle, specifically how they can fix carbon under these conditions under these conditions.

“While integrating educational opportunities into the data generated by the proposal is not a stipulation of the CSP program, this is truly is a commendable effort and it serves as a further metric of the dedication these authors obviously have for the work,” noted one reviewer regarding the proposal submitted.

Several fungal projects were also selected. One of them focuses on Aureobasidium pullulan, the genetic information from which could lead to the development of drought-tolerant and salt-tolerant crops. Proposed by Martina Turk and Nina Gunde-Cimerman of the University of Ljubljana in Slovenia, the fungus thrives in a variety of environments and has been found on plants, PVC pipes and even on the walls of the Chernobyl nuclear power plant. The genomic information could help researchers studying ionizing radiation to develop new methods of assessing radiation effects. Additionally, as recent studies indicate, a strain of this fungus has been found in Arctic glaciers, and researchers hope to learn more about its role in the carbon cycle, especially as these glacial habitats are being affected by climate change. From a bioenergy perspective, the yeast-like fungus may hold enzymes that can help break down biomass, underscoring the metabolic versatility of fungi and relevance to and the DOE mission.

Another fungal project is focused on developing a comparative transcriptomics pipeline and is led by Antonio Pisabarro of Spain’s Public University of Navarre. Using several brown rot and white rot fungi whose genomes either have been or are in the process of being sequenced by the DOE JGI for their relevance to bioenergy and carbon cycling, Pisabarro and his collaborators want to improve the process by which gene expressions and gene functions of these fungi are compared.

Finally, one of the metagenome projects involves the so-called termite of the sea, the shipworm. As a wood-boring bivalve, the shipworm has two bacterial populations that can break down — one in the gut and the other in a specialized organ in the gills. The DOE JGI sequenced the only shipworm species adapted to cold water — Bankia setacea – as part of the CSP 2009 portfolio to identify the enzymes in these microbes involved in breaking down wood for cellulosic biofuel production. Now DOE JGI collaborator Daniel Distel of the Ocean Genome Legacy Foundation has proposed studying both microbial communities in different species of shipworm, including Lyrodus pedicellatus, a shipworm species adapted to warm water. Wood-boring bivalves are the only marine animals known to sustain normal growth and reproduction feasting solely on wood.

See the complete list of CSP 2011 sequencing projects.

Follow the progress of these projects on Twitter and Facebook.

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:

JGI Contributes Nine to 2022 Highly Cited Researchers List

Nine headshots, one for each researcher, laid out beside a purple ribbon reading, "Home to Highly Cited Researchers 2022 Clarivate"

JGI announces first round of 2023 New Investigator awardees

Digital ID card with 10 headshots reads: Congratulations to our 2023 New Investigator recipients!

JGI at 25: Following Fungi that Pry Apart Plant Polymers

A brown goat with white horns looks at green hay

Exploring Possibilities: 2022 JGI-UC Merced Interns

2022 JGI-UC Merced interns (Thor Swift/Berkeley Lab)

JGI at 25: Using team science to build communities around data

JGI at 25: Expanding Metagenomics to Capture Viral Diversity

Artist rendering of genome standards being applied to deciphering the extensive diversity of viruses. (Illustration by Leah Pantea)
  • 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