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 › Characterizing Communities: JGI Announces Latest CSP Portfolio

October 1, 2019

Characterizing Communities: JGI Announces Latest CSP Portfolio

Proposals aim to sequence and annotate genomes from Antarctica to Africa to global oceans.

Laura Selbman of Italy’s University of Tuscia proposes to sequence nearly 100 species of black fungi in a 3-year effort called STRES (Shed light in The daRk lineagES of the Fungal Tree Of Life (FTOL)). Black fungi are ubiquitous in many environments – the collage shows examples of habitats colonized by these fungi - and extremely tolerant of stresses ranging from UV radiation to heat to toxic metals and organic pollutants.(Collage courtesy of L. Selbmann)

Laura Selbman of Italy’s University of Tuscia proposes to sequence nearly 100 species of black fungi in a 3-year effort called STRES (Shed light in The daRk lineagES of the Fungal Tree Of Life (FTOL)). Black fungi are ubiquitous in many environments – the collage shows examples of habitats colonized by these fungi – and extremely tolerant of stresses ranging from UV radiation to heat to toxic metals and organic pollutants.(Collage courtesy of L. Selbmann)

Through the Community Science Program of the U.S. Department of Energy (DOE) Joint Genome Institute (JGI), a DOE Office of Science user facility, 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.

Nearly 200 Terabases of data are expected to be generated for the accepted proposals, said Susannah Tringe, JGI User Programs Deputy. “These new CSP projects accelerate our efforts to characterize poorly-studied algal and viral genomes, and integrate with key DOE Office of Biological and Environmental Research (BER) initiatives in bioenergy crop improvement and terrestrial carbon transformations.”

The JGI’s large-scale call included algal genomics as a focus area, and one of the accepted proposals came from Chris Bowler of France’s Institut de Biologie. His team proposed to sequence Chaetoceros microalgae, or diatoms. Through the Tara Oceans Expeditions that took place between 2009 and 2013, the Chaetoceros genus has been identified as the most abundant in the world’s oceans, found in a wide range of morphologies and ecologies. Diatoms, Bowler’s proposal noted, are believed responsible for a fifth of the planet’s photosynthesis activities. Aside from being a key component of the marine food web base, they also feature in many nutrient cycles. Thus, having reference Chaetoceros genomes would provide more information on these ecologically relevant species.

Another focus area was inter-organismal interactions, and two fungal proposals focus on symbiotic relationships. Jessie Uehling of the University of California, Berkeley is interested in better characterizing the role endosymbiotic bacteria play on mating habits of Mucoromycota fungi, and their effects on these oil-producing species. Many fungi have beneficial symbiotic relationships with plants and bacteria; in many instances, fungal physiology is impacted by these bacteria during mating processes. Kathryn Bushley of the University of Minnesota is interested in learning more about the fungal endophytes of soybean and how they deter two significant pathogens, the soybean cyst nematode and the soybean sudden death pathogen.

Related to Uehling’s proposal: Transmission electron microscopy of Mycoavidus cysteinexigens (arrows) aggregated around lipid bodies (lb) inside hyphae of Mortierella elongata isolate NVP64. Scale bar 1 um. (Alessandro Desiro)

Related to Uehling’s proposal: Transmission electron microscopy of Mycoavidus cysteinexigens (arrows) aggregated around lipid bodies (lb) inside hyphae of Mortierella elongata isolate NVP64. Scale bar 1 um. (Alessandro Desiro)

In the genes-to-function focus area, Daniel Kliebenstein from the University of California, Davis proposes to develop high quality reference genomes for 10 individuals from each of the following five species: Camelina sativa, Thlaspi arvense (pennycress), Crambe hispanica, Brassica oleracea, and Streptanthus barbigeri (bearded jewelflower). Part of efforts to develop pangenomes for these species, this approach would also allow researchers to learn more about what is and is not modifiable in crops, which can help optimize crop improvements.

Some of the proposals were associated with more than one focus area of the proposal call. Richard Dick of The Ohio State University aims to study plant drought resilience in the Sahel, an arid region of West Africa. The staple crop there is millet, grown without fertilizer and under erratic rainfall conditions. To help mitigate drought, famers are growing millet with an indigenous shrub and these intercropping efforts appear to be redistributing water availability. By sequencing the millet rhizosphere and endosphere communities both with and without the shrub’s presence, researchers hope to learn more about the mechanisms that allow the millet to thrive in drought conditions. The proposal targets the CSP focus area in plant microbiomes, as well as those in inter-organismal interactions and terrestrial elemental cycling.

George diCenzo of Canada’s Queens University aims a multi-omics approach toward generating “with unprecedented precision” the gene functional networks and regulatory networks of a single strain of Sinorhizobium meliloti. S. meliloti is one of the rhizobia, a group of nitrogen-fixing bacteria with symbiotic relationships in plant roots of legume crops such as soybeans and peas. Their presence reduces the need to add fertilizers to the soil.

diCenzo’s proposal is also notable as he had an accepted new investigator proposal last year, and he noted that the experience proved beneficial for the large-scale call. “I am convinced that the experience writing the New Investigator proposal, and receiving feedback from reviewers, was invaluable in preparing the large-scale application. It provided practice in writing for the JGI and describing my general research area and its relevance to the JGI, and the feedback from reviewers allowed me to be better prepared and to avoid making the same mistakes,” he said. “Although in my specific case the projects are different for the two proposals, I can see the New Investigator program being a valuable “stepping-stone” to a large-scale proposal by allowing researchers to test a project on a smaller scale as a proof-of-concept or by allowing the generation of preliminary data for a larger study.”

The accepted proposals start October 1, 2019. See the full list of accepted proposals at https://jgi.doe.gov/our-projects/csp-plans/approved-proposals-fy20/.

 

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:

Introducing New Members of the JGI User Executive Committee

incoming 2023 UEC members

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

  • 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