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

Our Science
Home › Science Highlights › Celebrating the Eucalyptus Reference Genome

July 7, 2015

Celebrating the Eucalyptus Reference Genome

New Phytologist dedicates an entire issue to various research directions based on the tree genome.

The Science:

Building off the Eucalyptus grandis tree genome that researchers at the DOE Joint Genome Institute helped sequence and analyze, several researchers demonstrate the utility of the reference genome in the June 2015 special issue of New Phytologist.

screencap of June 2015 New Phytologist cover

The June 2015 issue of the journal New Phytologist was dedicated solely to the eucalyptus. (Credit for the journal’s Volume 206 Issue 4 cover image: Stand of Eucalyptus grandis trees near Kwambonambi, KwaZulu-Natal, South Africa. Courtesy of Alexander A. Myburg.)

The Impact:

Based on the reference eucalyptus genome, two major themes that scientists have focused on are described in a special issue of New Phytologist. These are that adaptive evolution can be applied to crop breeding for bioenergy applications, among others, and that the genome sequence enables the development of tools to further improve this genomic resource.

Summary

As a fast growing tree found in multiple continents, eucalyptus is of interest to the U.S. Department of Energy as a potential biofuel feedstock. For this reason, it was selected in 2008 as a Community Science Program project for the DOE Joint Genome Institute, a DOE Office of Science User Facility. In June 2014, an international consortium of researchers, including DOE JGI scientists, released the reference genome of Eucalyptus grandis. A brief video featuring Jerry Tuskan, a longtime DOE JGI collaborator at Oak Ridge National Lab, and a member of the original team who worked on the eucalyptus genome, can be viewed at http://bit.ly/eucalyptusTuskan.

In a showcase of how the global research community has already begun harnessing the eucalyptus genomic resources made available by the DOE JGI through the plant portal Phytozome, the June 2015 issue of New Phytologist was dedicated to all things eucalyptus. The effort was spearheaded by DOE JGI collaborator Zander Myburg of the University of Pretoria, one of the leads on the eucalyptus genome CSP project, and a co-author of several of the papers published in the special issue.

“Compared to plant genomes sequenced to date, [eucalyptus] represents an independent evolutionary experiment on what it means to be a large woody perennial plant evolving in diverse, and often stressful, habitats,” he and co-author Steven Strauss wrote in the lead commentary for the issue. “The papers in this issue show that the genome sequencing investment by the US Department of Energy – and the associated inputs and collaborative efforts from many scientific and industrial communities around the globe – is truly an accomplishment to celebrate.”

Several studies in the special issue focus on various features of the eucalyptus genome, primarily with an eye toward improving wood production for bioenergy applications, while others are analyses or tools that can further improve the reference genome. One such paper comes from French researchers who developed genetic maps that helped improve the eucalyptus reference assembly last year, and expands on that work. Ultimately, Eucalyptus could provide both a sustainable source of bioenergy through its wood, as well as multiple bioproducts based on its well-known oil content.

Contact

Alexander Myburg
University of Pretoria
Zander.Myburg@up.ac.za

Funding

  • U.S. Department of Energy Office of Science

Publication

  • Strauss SH et al. Plant scientists celebrate new woody plant genome. New Phytol. 2015 Jun;206(4);1185-7. doi: 10.1111/nph.13443.

Related Links

  • http://onlinelibrary.wiley.com/doi/10.1111/nph.2015.206.issue-4/issuetoc
  • http://onlinelibrary.wiley.com/doi/10.1111/nph.13443/abstract
  • http://jgi.doe.gov/why-sequence-the-eucalyptus-tree/
  • http://phytozome.jgi.doe.gov
  • http://bit.ly/eucalyptusTuskan
  • http://jgi.doe.gov/just-food-koalas-eucalyptus-global-tree-fuel-fiber/
  • http://jgi.doe.gov/eucalyptus-grandis-genome-2-0-community-resource/

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)

Filed Under: Science Highlights

More topics:

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

Related Content:

Soil virus offers insight into maintaining microorganisms

Silver age of GOLD introduces new features

Abstract image of gold lights and squares against a black backdrop

Virus Discoveries that Keep Getting Bigger

And illustration of a giant virus in purple and blue tones.

Model fern reveals insight into DNA thievery in ferns

A green fern against a black backdrop

Understanding Wildfire Recovery, Starting in Soil

A photograph of the forest floor, covered in pine needles, with burned trees in the background.

Extracting the Secrets of Secondary Metabolites

A graphic flowchart showing how CRAGE and CRISPR work together
  • 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