DOE Joint Genome Institute

  • COVID-19
  • About Us
  • Contact Us
  • Our Science
    • DOE Mission Areas
    • Science Programs
    • Science Highlights
    • Scientists
    A vertical tree stump outdoors with about a dozen shiitake mushrooms sprouting from its surface.
    Tracing the Evolution of Shiitake Mushrooms
    Understanding Lentinula genomes and their evolution could provide strategies for converting plant waste into sugars for biofuel production. Additionally, these fungi play a role in the global carbon cycle.

    More

    Soil Virus Offers Insight into Maintaining Microorganisms
    Through a collaborative effort, researchers have identified a protein in soil viruses that may promote soil health.

    More

    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

  • Our Projects
    • Search JGI Projects
    • DOE Metrics/Statistics
    • Approved User Proposals
    • Legacy Projects
    The switchgrass diversity panel growing at the Kellogg Biological Station in Michigan. (David Lowry)
    Mapping Switchgrass Traits with Common Gardens
    The combination of field data and genetic information has allowed researchers to associate climate adaptations with switchgrass biology.

    More

    Artist rendering of genome standards being applied to deciphering the extensive diversity of viruses. (Illustration by Leah Pantea)
    Expanding Metagenomics to Capture Viral Diversity
    Along with highlighting the viruses in a given sample, metagenomics shed light on another key aspect of viruses in the environment — their sheer genetic diversity.

    More

    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

  • Data & Tools
    • IMG
    • Data Portal
    • MycoCosm
    • PhycoCosm
    • Phytozome
    • GOLD
    Abstract image of gold lights and squares against a black backdrop
    Silver Age of GOLD Introduces New Features
    The Genomes OnLine Database makes curated microbiome metadata that follows community standards freely available and enables large-scale comparative genomics analysis initiatives.

    More

    Graphical overview of the RNA Virus MetaTranscriptomes Project. (Courtesy of Simon Roux)
    A Better Way to Find RNA Virus Needles in the Proverbial Database Haystacks
    Researchers combed through more than 5,000 data sets of RNA sequences generated from diverse environmental samples around the world, resulting in a five-fold increase of RNA virus diversity.

    More

    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

  • User Programs
    • Calls for Proposals
    • Special Initiatives & Programs
    • Product Offerings
    • User Support
    • Policies
    • Submit a Proposal
    Digital ID card with six headshots reads: Congratulations to our 2022 Function Genomics recipients!
    Final Round of 2022 CSP Functional Genomics Awardees
    Meet the final six researchers whose proposals were selected for the 2022 Community Science Program Functional Genomics call.

    More

    CSP New Investigators FY23 R1
    JGI Announces First Round of 2023 New Investigator Awardees
    Twice each year we look for novel research projects aligned with DOE missions and from PIs who have not led any previously-accepted proposals through the CSP New Investigator call.

    More

    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

  • News & Publications
    • News
    • Blog
    • Podcasts
    • Webinars
    • Publications
    • Newsletter
    • Logos and Templates
    • Photos
    2022 JGI-UC Merced interns (Thor Swift/Berkeley Lab)
    Exploring Possibilities: 2022 JGI-UC Merced Interns
    The 2022 UC Merced intern cohort share how their summer internship experiences have influenced their careers in science.

    More

    Using Team Science to Build Communities Around Data
    As the data portals grow and evolve, the research communities further expand around them. But with two projects, communities are forming to generate high quality genomes to benefit researchers.

    More

    Cow Rumen and the Early Days of Metagenomics
    Tracing a cow rumen dataset from the lab to material for a hands-on undergraduate research course at CSU-San Marcos that has since expanded into three other universities.

    More

News & Publications
Home › News Releases › 2021 JGI Proposal Call Brings New Investigators into Community Science Program

October 8, 2020

2021 JGI Proposal Call Brings New Investigators into Community Science Program

Accepted proposals emphasize JGI interests in algae and secondary metabolites.

Scanning electron micrographs of diverse diatoms. (Credits: Diana Sarno, Marina Montresor, Nicole Poulsen, Gerhard Dieckmann)

Scanning electron micrographs of diverse diatoms. (Credits: Diana Sarno, Marina Montresor, Nicole Poulsen, Gerhard Dieckmann)

A total of 27 proposals have been approved through the annual Community Science Program (CSP) call of 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 accepted proposals come from 80 full proposals, resulting from 95 letters of intent. For the first time, 63 percent of the accepted proposals come from investigators who have not previously been a principal investigator (PI) on an approved JGI proposal.

Approved proposals make use of JGI’s breadth of capabilities while also highlighting collaborative research of a scale exceeding a single lab’s capacity. Additionally, the call recommended including plans to analyze and distribute data through the DOE Systems Knowledgebase (KBase), a free, open source data science platform that allows users to explore data and share reproducible analyses with collaborators and the broader community.

High oleic pennycress. (Courtesy of Ratan Chopra)

High oleic pennycress. (Courtesy of Ratan Chopra)

The approved proposal from Alex Harkess of Auburn University started as a small-scale white paper focused on duckweed through the CSP New Investigator call. It is the first project to have successfully evolved into a full-scale proposal known as the Brassicales Genome Initiative. Brassicales is represented by more than 4,700 species, and the proposal focuses on investigating the repeated evolution of three traits relevant to DOE interests: photosynthetic transitions, specialized metabolites, and woodiness.

A proposal from Ben Shen of The Scripps Research Institute (TSRI) launches a collaborative effort between JGI, TSRI and the University of Minnesota to establish the Natural Products Genomics Resource Center. To help enable the discovery of secondary metabolites, also referred to as natural products, the proposal includes plans to sequence several thousand Actinobacteria strains and then use computational tools to analyze biosynthetic gene clusters and then develop them for a range of applications. (Hear Ben Shen here in the JGI Natural Prodcast podcast.)

Red algal life at the extremes. Left: Cyanidiophyceae thriving in hot springs at Yellowstone National Park at Yellowstone National Park. Right: Rock dwelling Galdeiereia phelgrea (green band in image) growing near Yellowstone hot springs. (D. Bhattacharya)

Red algal life at the extremes. Left: Cyanidiophyceae thriving in hot springs at Yellowstone National Park at Yellowstone National Park. Right: Rock-dwelling Galdeiereia phelgrea (green band in image) growing near Yellowstone hot springs. (D. Bhattacharya)

Several accepted proposals reflect JGI’s interest in algal research for bioenergy production and algae’s roles in nutrient cycling, now a facet of the Fungal & Algal Program. For example, green algae represent the largest group of primary producers generating organic compounds through photosynthesis, but only a fraction have been sequenced. Adriana Lopes dos Santos from Singapore’s Nanyang Technological University aims to generate genome sequences from underrepresented green algae groups in a wide range of environments. A similar proposal focused on diatom genomes from Thomas Mock of the University of East Anglia was also approved to learn more about the roles of diatoms in carbon fixation and in aquatic food webs. Finally, Debashish Bhattacharya of Rutgers University is interested in understanding how unicellular red algae (Cyanidiophyceae) have adapted thrive in environments including hot springs and acid mining sites, traits that might have biotechnological applications.

Expansin complex with cell wall in background. (Courtesy of Daniel Cosgrove)

Expansin complex with cell wall in background. (Courtesy of Daniel Cosgrove)

Among the other accepted proposals:

  • Amanda Hurley and Jo Handelsman of the Wisconsin Institute for Discovery (WID) are interested in sequencing secondary metabolite-producing environmental bacteria from the Tiny Earth collection. The work builds upon a pilot project to sequence antimicrobial-producing strains. Established by Handelsman, Tiny Earth aims to crowdsource antimicrobial discovery for the control of plant pathogens, partnering with 600 instructors worldwide who work with more than 10,000 undergraduate students each year.
  • Brian Looney of Duke University is interested in understanding which species of mycorrhizal fungi are important for poplar plant health, in part to learn how these species can modulate their behavior in the presence of other fungi. Poplar is a JGI Flagship Plant, of interest as a candidate bioenergy feedstock.
  • John McKay of Colorado State University is interested in developing mutant populations of the bioenergy feedstock crop Camelina sativa, and generating their genome sequences to improve breeding by genetic improvements.
  • Apomixis is asexual reproduction through seeds, and Peggy Ozias-Akins from the University of Georgia is interested sequencing relatives of switchgrass that are apomictic. This trait would be beneficial for reproduction of improved heterozygous clones through seed.
  • Eric Wommack of the University of Delaware is interested in learning how environmental conditions influence viral-host interactions in three groups: cyanophages, bacteriophages, and giant algal viruses.
Hot spring in Yellowstone National Parks' Artist Paint Pot area. (Courtesy of Roland Hatzenpichler)

Hot spring in Yellowstone National Parks’ Artist Paint Pot area. (Courtesy of Roland Hatzenpichler)

The approved proposals started October 1, 2020 and the full list is available here. They are expected to generate publicly available data relevant to DOE interests in finding solutions to energy and environmental challenges, and be of use to the larger research community.

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:

Supercharging SIP in the Fungal Hyphosphere

Green plant matter grows from the top, with the area just beneath the surface also visible as soil, root systems and a fuzzy white substance surrounding them.

New Research Sheds Light on Diversity in the Deep Sea

A photo taken in the deep sea. Black clouds billow out of hydrothermal vents.

Sequencing Sphagnum Leads to Discovery of Sex Chromosomes

A photo of two sphagnum species: S. divinum (red) and S. angustifolium (green)]

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!
  • 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