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 › Revealing Aspergillus Diversity for Industrial Applications

February 27, 2017

Revealing Aspergillus Diversity for Industrial Applications

Comparative analysis of Aspergillus species provides genus-wide view of fungal diversity

In the world of fungi, Aspergillus is an industrial superstar. Aspergillus niger, for example, has been used for decades to produce citric acid—a compound frequently added to foods and pharmaceuticals —through fermentation at an industrial scale. Other species in this genus play critical roles in biofuel production, and plant and human health. Since the majority of its 350 species have yet to be sequenced and analyzed, researchers are still at the tip of the iceberg when it comes to understanding Aspergillus’ full potential and the spectrum of useful compounds they may generate.

In a study published February 14, 2017 in the journal Genome Biology, an international team including researchers at the U.S. Department of Energy Joint Genome Institute (DOE JGI), a DOE Office of Science User Facility, report sequencing the genomes of 10 novel Aspergillus species, more than doubling the number of Aspergillus species sequenced to date. The newly sequenced genomes were compared with the eight other sequenced Aspergillus species. With this first ever genus-wide view, the international consortium found that Aspergillus has a greater genomic and functional diversity than previously understood, broadening the range of potential applications for the fungi considered one of the most important workhorses in the biotechnology.

“Several Aspergillus species have already established status as cell factories for enzymes and metabolites. However, little is known about the diversity in the species at the genomic level and this paper demonstrates how diverse the species of this genus are,” said study lead author Ronald de Vries of the Westerdijk Fungal Biodiversity Institute in the Netherlands. “One can’t assume that an Aspergillus species will have the same physiology as a better studied species of the genus.”

Comparative growth of aspergilli. (Ad Wiebenga & Ronald de Vries, Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands)

Comparative growth of aspergilli. (Ad Wiebenga & Ronald de Vries, Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands)

The study, conducted through the DOE JGI’s Community Science Program, also demonstrates the importance of evaluating biodiversity within a genus to understand how fungi can be greater utilized to solve a variety of problems.

A Catalog of Enzymes for Biotechnological Applications

Sequencing a diverse set of Aspergillus genomes allows researchers to build a more comprehensive catalog of enzymes for biotechnological applications, added DOE JGI Fungal Genomics Program Head Igor Grigoriev, senior author of the paper. Those applications include harnessing Aspergillus to help protect crops and ward off agents that can cause diseases in plants.

Comparing the newly sequenced genomes to those already available, researchers found a huge variety of carbohydrate-active enzymes (CAZymes) among the Aspergillus species, suggesting distinct strategies to break down plant biomass. CAZymes are responsible for breaking down plant cell walls, useful for industrially processing plants the DOE considers candidate bioenergy crops. The sugars that are part of these cell walls can’t be accessed and fermented to make biofuels unless the walls are broken down by agents like CAZymes.

“Each of these 10 genomes encodes for a unique composition of CAZymes—and the wider assortment helps formulate enzyme cocktails better suited for different types of plant biomass to efficiently convert them into biofuels,” Grigoriev said.

In addition to biofuels, CAZymes can also help facilitate the production of paper, textiles, food, feed and pharmaceuticals, according to de Vries.

Pursuing a Deeper Exploration

The comparative analysis between the genomes also enabled researchers to uncover a high diversity of genes that: 1) allow the fungi to produce secondary metabolites, compounds that may be useful for applications such as crop protection; and, 2) enable the fungi to tolerate stress. The knowledge gained in secondary metabolism and stress response will help to provide more insight in the mechanisms underlying these functions.

But despite the new insights gained, de Vries emphasizes that much still remains unknown about the full spectrum of what Aspergillus can do. “There is [still] much to learn and get from a better study [of Aspergillus],” he said. “The potential for applications within the genus has barely been touched.”  Grigoriev adds: “Encouraged by results of this study we now pursue a deeper exploration of the Aspergillus genus, sequencing the remaining 300 species, each carrying a unique composition genes, enzymes, and pathways.”

All of the fungal genomes are available on the DOE JGI’s Fungal Genomics portal MycoCosm. Letters of Intent are currently being accepted for the DOE JGI Community Science Program (CSP) and must be submitted online by March 31, 2017. The CSP Annual Call is focused on large-scale sequence-based genomic science projects that address questions of relevance to DOE missions in energy security and sustainability and global biogeochemistry. Click here for more information regarding the CSP call.

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:

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!

Introducing New Members of the JGI User Executive Committee

incoming 2023 UEC members

JGI at 25: Mapping Switchgrass Traits with Common Gardens

Aerial photo of the switchgrass diversity panel late in the 2020 season at the Kellogg Biological Station in Michigan. (Robert Goodwin)

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"
  • 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