DOE Joint Genome Institute

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

    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.

    More

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

    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.

    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
    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

    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.

    More

About Us
Home › About Us › Annual Progress Report › 2021 JGI Progress Report
  • People
  • Location
  • History
  • Partners
  • Committees
  • Ops Expenses
  • Progress Report
  • Diversity
  • Workforce Development

2021 JGI Progress Report

Animated image of the Integrative Genomics Building, home of the DOE Joint Genome Institute.

The Integrative Genomics Building (IGB) seen above is home to the  U.S. Department of Energy (DOE) Joint Genome Institute (JGI), a DOE Office of Science User Facility located at Lawrence Berkeley National Laboratory (Berkeley Lab), the DOE Systems Biology Knowledgebase (KBase), and the National Microbiome Data Collaborative (NMDC). Berkeley Lab Biosciences Area researchers are also co-located in the IGB.

The JGI vision and mission statement.

The interactions between plants and the microbes in and around their roots influence plant health and development. Using controlled fabricated ecosystems or EcoFABs such as the one shown here help researchers conduct studies with reproducible parameters.

Director’s Perspective

Nigel Mouncey, Director, DOE Joint Genome Institute

In 2021, several researchers and staff supporting the JGI user community were recognized by multiple organizations.

Science Highlights

Mingqin “Mike” Shao in the plant room at the IGB checking one of the JGI flagship genome species, Brachypodium distachyon.

Green millet (Setaria viridis) plant collected in the wild. (Courtesy of the Kellogg lab) Shattering Expectations: Novel Seed Dispersal Gene Found in Green Millet

Researchers at the Danforth Center, the JGI and the HudsonAlpha Institute for Biotechnology released a very high-quality reference green millet genome sequence and identified a gene related to seed dispersal in wild populations.

Female (left) and male (right) Ceratodon purpureus plants. Females typically grow larger than males in several traits, like the length of leaves. Males often turn red when developing antheridiophores, which in mosses are the structures that produce sperm (seen in the bottom right. (Sarah Carey) The Case for Conservation

The genome assemblies of high-quality reference sequences for the male and female fire moss plants (Ceratodon purpureus) are a testament to the multiple advances in sequencing technologies applied to the effort.

The anaerobic fungus Anaeroromyces robustus growing on reed canary grass. (Vaithiyalingam Shutthanandan, PNNL/EMSL) Gut Fungi: Unexpected Source of Novel Chemicals

Combing through the genomes of four anaerobic fungal species has revealed, for the first time, that this group is unexpectedly powerful: they can whip up dozens of complex natural products, including new ones.

The study site in the coniferous forest located in the Bohemian Forest National Park, Czech Republic. (Petr Baldrian) Bacteria and Fungi Divvy Up the Work in Forest Floor

By analyzing the enzymes present in the complex organic matrix of the forest floor, researchers found that fungi are more active in degrading plant matter, and bacteria are more active in fixing and metabolizing nitrogen.

From Sekimoto et al., 2011: Olpidium bornovanus, a unicellular fungus, is an obligate parasite of plants that reproduces with flagellated, swimming zoospores. A-B. Vegetative unicellular thalli in cucumber root cells. Thalli differentiate into sporangia with zoospores, or into resting spores. C. An empty sporangium, after zoospore release. D. A thick-walled resting spore. E. Zoospores being released from a sporangium, showing the sporangium exit tube (arrowheads). F. A swimming zoospore with a single posterior flagellum. G. An encysted zoospore. Bars: A-E = 10 μm; F,G = 5 μm. (Figures are from Sekimoto et. al., 2011 used under a Creative Commons Attribution 2.0 License.) Olpidium, The Key to the Origin of Terrestrial Fungi

Taking advantage of the rapid development of binning methods, and with much more extensive taxonomic and genetic sampling, researchers confirmed the affinity between Olpidium and the non-flagellated terrestrial fungi. 

Boeuf and colleagues collected samples of SAR324 microbial communities from this research vessel, the Kilo Moana. (School of Ocean And Earth Science And Technology at University of Hawaii at Manoa) Marine Microbe Contains Multitudes

In the ocean’s North Pacific Subtropical Gyre, microbes tend to stay localized at different depths. Scientists looked into how the bacterium SAR324 can be found throughout the water column.

Unicellular algae in the Chlorella genus, magnified 1300x. (Andrei Savitsky) A One-Stop Shop for Analyzing Algal Genomes

PhycoCosm’s interactive browser allows researchers to look deep into more than 100 algal genomes. The genome portal reinforces the JGI’s new strategic focus on exploring algal biology, diversity, and ecology.

Scientists sample a brown mat of aggregated phytoplankton. (Katrin Schmidt) Climate Change Threatens Base of Polar Oceans’ Bountiful Food Webs

An international research team reported warm-adapted microbes edging polewards and may be displacing resident tiny algae much more easily than previously suspected. The trend could destabilize the delicate marine food web.

Algae growing in a bioreactor. (Dennis Schroeder, NREL) Refining the Process of Identifying Algae Biotechnology Candidates

JGI, LANL and NREL researchers combined expertise 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.

Screencap of green algae video for PNAS paper Green Algae Reveal One mRNA Encodes Many Proteins

Gene expression in eukaryotes was long held to be monocistronic; a single gene makes messenger RNA, which encodes a single protein. Researchers have found numerous examples of polycistronic expression in green algae.

Artistic interpretation of CheckV assessing virus genome sequences from environmental samples. (Rendered by Zosia Rostomian​, Berkeley Lab) An Automated Tool for Assessing Virus Data Quality

A command-line tool called CheckV can be broadly utilized to gauge virus data quality. It helps researchers to follow best practices and guidelines for providing the minimum amount of information for an uncultivated virus genome.

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

Researchers discovered that “diversity generating retroelements” (DGRs) in viruses are not only widespread, but also surprisingly active. They appear to generate diversity quickly, allowing these viruses to target new microbial prey.

Image of biofilm with both Altiarchaea (blue) and viruses (red). (Victoria Turzynksi and Lea Griesdorn) Plotting a Model for Virus-Host Warfare Deep Below Ground

Altiarchaea counter multiple attempts at virus infections because their genomes include sequences that code for CRISPR systems. These help bacteria resist foreign genetic elements by incorporating fragments from infecting viruses and phages.

JGI-developed genetic engineering technique CRAGE lands the cover of ACS Synthetic Biology. (Wayne Keefe/Berkeley Lab) An Age of CRAGE: Advances in Rapidly Engineering Non-model Bacteria

The JGI has demonstrated CRAGE as a versatile engineering system that allows scientists to conduct genome-wide screens and explore biosynthetic pathways. Now CRAGE is being applied to other synthetic biology problems.

(PXFuel) Designer DNA: JGI Helps Users Blaze New Biosynthetic Pathways

A special issue of the journal Synthetic Biology puts the spotlight on JGI’s DNA design and synthesis superpower. In a series of case studies, scientific users share what they’ve discovered through their collaborations.

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”

In work enabled by the JGI’s Emerging Technologies Opportunity Program (ETOP), The University of Texas at Austin and Northwestern University researchers show yeast metabolic pathways work outside the cell environment.

Impact: By the Numbers

Animated image of Diane Bauer watching a liquid handler processing samples

This image shows Diane Bauer monitors a liquid handler processing sequencing samples. The JGI generated a record 467 Terabases of sequence in FY2021.

Spending Profile FY2021

Users on the Map: 2,180

North America 1,541 Denmark 11 Slovenia 2 Japan 19
United States 1,444 Estonia 2 Spain 40 Malaysia 1
Canada 92 Finland 13 Sweden 19 Oman 1
Mexico 5 France 55 Switzerland 11 Singapore 3
Germany 95 United Kingdom 56 South Korea 5
South America 28 Greece 3 Taiwan 2
Argentina 1 Hungary 11 Africa 12 Vietnam 1
Brazil 20 Iceland 1 Morocco 2
Chile 1 Ireland 3 Nigeria 1 Australia & New Zealand 58
Colombia 2 Italy 31 South Africa 8 Australia 47
Uruguay 4 Netherlands 26 Tunisia 1 New Zealand 11
Norway 22
Europe 451 Poland 3 Asia 90
Austria 11 Portugal 8 China 36
Belgium 16 Russia 5 India 13
Czech Republic 5 Serbia 2 Israel 9

Users on the U.S. Map: 1,444

 

Cumulative Number of Projects Completed

Cumulative Number of Scientific Publications

Sequence Output

(in billions of bases or GB)

The JGI supports short- and long-read sequencers, where a read refers to a sequence of DNA bases. Short-read sequencers produce billions of paired-end 150 basepair reads used for quantification, such as in gene expression analysis. Long-read sequencers currently average 60,000–70,000 bp reads and are used for de novo genome assembly. Combined short-read and long-read totals per year give JGI’s annual sequence output. The total sequence output in 2021 was 467,195 GB.

Sequencing Productivity

Billions of Base Pairs

User Letters of Intent/Proposals Submitted & Approved

Computational Infrastructure

The JGI has generated petabytes of high-quality sequence data and analysis; rapid and smooth access to the public datasets by the research community is enabled by high-performance computing resources and infrastructure.  In this image, NERSC engineer James Botts studies a computer system cluster.

JGI Archive and Metadata Organizer (JAMO)

11,010 million file records

JAMO Archived Data Footprint

11.683 Petabytes (PB)

Data Downloads in FY21

4.201 million files; 1.646 PB

Users of JGI Tools & Data

The Genome Portal provides unified access to all JGI genomic databases and analytical tools. A user can search, download and explore multiple data sets available for all JGI sequencing projects including their status, assemblies, and annotations of sequenced genomes. Launched in FY2021, the Data Portal allows JGI users to more easily access public data sets through a common set of metadata across the files that are submitted by each scientific program. The Genome Portal will be retired once the same features are available on Data Portal.

Photography and cinemagraphs by Thor Swift, Berkeley Lab. Design by Creative Services, IT Division, Berkeley Lab.

  • 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

© 1997-2022 The Regents of the University of California