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 › A Better Way to Find RNA Virus Needles in the Proverbial Database Haystacks

September 30, 2022

A Better Way to Find RNA Virus Needles in the Proverbial Database Haystacks

Graphical overview of the RNA Virus MetaTranscriptomes Project. (Courtesy of Simon Roux)

Graphical overview of the pipeline starting with the RNA Virus MetaTranscriptomes (RVMT) database to uncover the expansion in RNA virus diversity. (Courtesy of Simon Roux)

Team develops a computational pipeline to sift and characterize RNA virus sequences. 

 

A zoo once offered a coloring book featuring polar bears in winter scenes that came with crayons in various shades of white. To researchers searching for sequences of RNA viruses in large data sets, their work may be akin to finding a single snowflake on a colored-in page of that book.

Published online September 28, 2022, in Cell, a team led by researchers at Tel Aviv University in Israel, the National Center for Biotechnology Information, and 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) describe a computational pipeline that can specifically scan for those snowflakes, or RNA virus sequences. Using this workflow, the team combed through more than 5,000 data sets of RNA sequences (metatranscriptomes) generated from diverse environmental samples around the world, resulting in a five-fold increase of RNA virus diversity.

“The world of viruses around us is vast, and we now have the means to explore it,” said Eugene Koonin, a senior investigator at the NCBI and one of the senior authors on the paper, of the uncovered viral diversity. “Although the technical challenges of data analysis at this scale are formidable.”

Computational Sieves to Filter Sequences

There are more microbes on the planet than particles in a handful of dirt, and viruses vastly outnumber the microbes. Advances in sequencing technologies and computational tools have uncovered a diversity of viruses that infect not just crops, animals and humans, but also microbes whose presence or absence can impact the planet’s nutrient cycles.

While most organism’s genetic information is encoded in DNA, with RNA delivering the instructions inside DNA to the cell, RNA viruses store their genetic information in RNA without a DNA stage. “I would argue RNA viruses globally are even less known than DNA viruses,” said Simon Roux, a JGI scientist and one of the project co-leads. “But same as DNA viruses, RNA viruses infect microbes all across the world and lead to cell death and/or profound changes in the cell physiology during infection.”

While all RNA viruses have a gene that encodes for an enzyme called RNS-directed RNA Polymerase (RdRP), necessary for replicating the RNA genome replication, detecting it has been a challenge. Finding the RNA virus snowflakes in the snowstorm of genomic data involved developing special computational sieves to filter out sequences that were unlikely to contain the RdRP sequence.

The work resulted from a three-way collaboration that began in 2019, recalled Uri Neri of Tel Aviv University, one of the project co-leads and first author of the study. Members of the Tel Aviv and NCBI teams, who were already working on mining prokaryotic viruses together, learned from JGI’s Nikos Kyrpides that his Microbiome Data Science group was also working on RNA virus mining. After a couple of virtual meetings of the three teams it was clear that a larger collaborative effort would be far more effective in achieving higher quality results compared to smaller individual efforts. This is also the type of synergistic and collaborative community spirit that the JGI advocates for and actively promotes.

The team used all the publicly available metatranscriptome datasets from the JGI’s Integrated Microbial Genomes & Microbiomes (IMG/M) system. “We then looked into many more samples and refined our methodology,” Neri said. “Our team grew and so did the scope of the project.” To this end, Kyrpides emphasized, the contributions of the numerous JGI science users in collecting and submitting their microbiome samples for sequencing at the JGI cannot be overstated. Their cooperation and support, he said, and in several cases, their permission to use yet unpublished sequence data, was absolutely critical for the success of this effort and so was the acknowledgement of their contribution.

Both Roux and Koonin noted that the plethora of RNA virus sequences uncovered “significantly changes the global view of virus diversity,” though not at the higher-level classifications of virus groups (phyla.) The new sequences are filling in some gaps on existing virus groups while also adding new branches. Additionally, RNA viruses do not appear to be evenly distributed around the world.

One expanded group is of viruses associated with bacteria; until now, most of the known RNA viruses have been associated with eukaryotes. Along with the expansion of bacteria-associated RNA viruses is the finding that “a few bacteria use CRISPR to defend against RNA,” Roux noted, “although it’s unclear why this is so rarely detected.”

Developing Approaches for Reconciling “Real” Big Data

For the team, the computational work that led to the uncovered abundance of RNA viruses is just the beginning. “I often say that just identifying a sequence as viral is not even half the story.” Neri said. “We invested a lot of our efforts into the post-discovery analyses – as best we could, we tried to describe the protein domains every virus carries, and who is their likely host. We’ve made all of that information fully free and openly available to the broader scientific community.”

Uri Gophna from Tel Aviv University, and Koonin both noted that other research in parallel has reported similar “dramatic expansions” of the global RNA virome. “We now need to compare and reconcile the findings, coming up with a single, non-redundant dataset,” said Koonin. “Hopefully, relatively soon we will be able to estimate the actual size of the RNA virome However, this is now real Big Data, we are dealing with billions of sequences, and soon, with trillions. The development of efficient, automated approaches to analyze and classify sequence data at this scale is essential.”

Researchers from the University of Oxford (UK), Vilnius University (Lithuania), J. Craig Venter Institute, Scripps Institute of Oceanography, Pennsylvania State University, Carnegie Institute for Science, Institut Pasteur (France), and Oregon State University were also involved in the work. Other authors on the paper are Uri Neri, Yuri I. Wolf, Antonio Pedro Camargo, Benjamin Lee, Darius Kazlauskas, I. Min Chen, Natalia Ivanova, Lisa Zeigler Allen, David Paez-Espino, Donald A. Bryant, Devaki Bhaya, RNA Virus Discovery Consortium, Mart Krupovic, and Valerian V. Dolja.

 

Publication: Neri U, Wolf Y, Roux S et al. Expansion of the global RNA virome reveals diverse clades of bacteriophages. Cell. 2022 Sept 28. doi:10.1016/j.cell.2022.08.023

 

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