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    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.

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    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.

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    Algae growing in a bioreactor. (Dennis Schroeder, NREL)
    Refining the Process of Identifying Algae Biotechnology Candidates
    Researchers combined expertise at the National Labs to screen, characterize, sequence and then analyze the genomes and multi-omics datasets for algae that can be used for large-scale production of biofuels and bioproducts.

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    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.

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    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.

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    Ian Rambo, graduate student at UT-Austin, was a DOE Graduate Student Research Fellow at the JGI
    Virus-Microbe Interactions of Mud Island Mangroves
    Through the DOE Office of Science Graduate Student Research (SCGSR) program, Ian Rambo worked on part of his dissertation at the JGI. The chapter focuses on how viruses influence carbon cycling in coastal mangroves.

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    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.”

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    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.

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    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.

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    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.

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    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.

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    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.

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    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.

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    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.

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    Integrating JGI Capabilities for Exploring Earth’s Secondary Metabolome
    Natural Prodcast podcast: Nigel Mouncey
    JGI Director Nigel Mouncey has a vision to build out an integrative genomics approach to looking at the interactions of organisms and environments. He also sees secondary metabolism analysis and research as a driver for novel technologies that can serve all JGI users.

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News & Publications
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April 20, 2020

Picking Up Threads of Cotton Genomics

cotton boll G. hirsutum (Cotton Inc)In Nature Genetics, a multi-institutional team has sequenced and assembled the genomes of the major cotton lineages. [Read More]

January 22, 2020

Here, There and Everywhere: Large and Giant Viruses Abound Globally

Art illustration capturing giant virus genomic diversity. (Zosia Rostomian/Berkeley Lab)JGI-led team significantly expands the global diversity of large and giant viruses. While the microbes in a single drop of water could outnumber a small city’s population, the number of viruses in the same drop—the vast majority not harmful to humans could be even larger. Viruses infect bacteria, archaea and eukaryotes, and they range in… [Read More]

January 21, 2020

Inspiring STEM Careers Through a Hands-on Everglades Microbiome Study

Students in the 2018 Boca Raton Community High School A-Level Advanced International Certificate of Education (AICE) Biology class collected samples from the Arthur R. Marshall Loxahatchee National Wildlife Refuge for the pilot project between the class and the JGI. (Image courtesy of Jon Benskin)Journal publication caps JGI pilot project with fledgling Florida high school scientists. The Florida Everglades evokes images of fanboats skimming over swamps, while alligators peer through the waters and clouds of insects hover just above. Described as a “river of grass” that stretches some 580,000 square miles across southern Florida, they encompass a wide range… [Read More]

October 1, 2019

Characterizing Communities: JGI Announces Latest CSP Portfolio

Proposals aim to sequence and annotate genomes from Antarctica to Africa to global oceans. 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… [Read More]

September 10, 2019

What Happens Underground Influences Global Nutrient Cycles

DOE user facilities EMSL and JGI announce FY 2020 collaborative FICUS projects. Through the Facilities Integrating Collaborations for User Science (FICUS) program, two Department of Energy (DOE) Office of Science national user facilities—the Environmental Molecular Sciences Laboratory (EMSL) and the DOE Joint Genome Institute (JGI)—have selected 11 proposals for support from 53 received through a… [Read More]

July 22, 2019

Learning to Look

Machine learning approach significantly expands inovirus diversity. To answer the question, “Where’s Waldo?” readers need to look for a number of distinguishing features. Several characters may be spotted with a striped scarf, striped hat, round-rimmed glasses, or a cane, but only Waldo will have all of these features. As described July 22, 2019, in Nature… [Read More]

December 17, 2018

Defining Quality Virus Data(sets)

Artist rendering of genome standards being applied to deciphering the extensive diversity of viruses. (Illustration by Leah Pantea)International consortium offers guidelines, best practices for characterizing uncultivated viruses. Microbes in, on and around the planet are said to outnumber the stars in the Milky Way Galaxy. The total number of viruses is expected to vastly exceed even that calculation. While many viruses remain unknown and uncultivated, advances in genome sequencing and analyses have… [Read More]

November 19, 2018

Hidden Giants in Forest Soils

One of the heated plots at the Harvard Forest (Jeff Blanchard)A surprising wealth of novel giant viruses has been found in a soil ecosystem. Characterizing the diversity of microbial cells in a handful of soil is so complex it was considered impossible. To date, only a small fraction of the microbes residing in, on and around soils have been identified as part of efforts to… [Read More]

November 14, 2018

Symbiosis a Driver of Truffle Diversity

Truffe noire du Peěrigord (Tuber melanosporum). (Francis Martin)Insights from a comparative analysis of five truffle-forming fungal species. While the sight of black or white truffles being shaved over on pasta is generally considered a sign of dining extravagance, they play an important role in soil ecosystem services. Truffles are the fruiting bodies of the ectomycorrhizal (ECM) fungal symbionts residing on host plant… [Read More]

October 30, 2018

Probing Interactions Among Molecular Mechanisms, Cellular Processes, and Elemental Cycles

Cropped image of switchgrass microcosm showing established root network. (James Moran)DOE user facilities EMSL and JGI announce FY 2019 collaborative FICUS projects. Two Department of Energy user facilities, the Environmental Molecular Sciences Laboratory (EMSL) and the Joint Genome Institute (JGI), have selected 12 of the 41 proposals received from a joint call for 2019 research under the Facilities Integrating Collaborations for User Science (FICUS) initiative…. [Read More]
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