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 › 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:

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