DOE Joint Genome Institute

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    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.

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

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    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.

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    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.

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    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.

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    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.

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    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.

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    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.

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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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    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.

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    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.

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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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    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.

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    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.

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    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.

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Upcoming Events

Events

The JGI is represented at conferences year round. Learn about events JGI is hosting, or where our researchers will be presenting next:

  • AAAS Meeting in Washington D.C., March 2-5, 2023
  • Fungal Pathogen Genomics in Hinxton, UK, May 9-13, 2023
  • SynBioBeta in Oakland, Calif., May 23-25, 2023
  • Sequencing to Function: Analysis and Applications for the Future (SFA2F) Meeting in Santa Fe, New Mexico, June 21-23, 2023
  • 2023 JGI Annual Meeting and workshops in Berkeley, Calif. and online, August 21-25, 2023
  • SACNAS National Diversity in STEM in Portland, Ore., October 26-28, 2023
  • NeLLi Symposium in Berkeley, Calif. and online, August 24-25, 2023

Past Events

  • Microbial Genomics & Metagenomics (MGM) Workshop, January 30-February 3, 2023
  • PAG Conference, January 13-16, 2023
  • SIMB Natural Products, January 8-12, 2023
  • The 2022 Annual User Meeting, August 29-31, 2022
  • VEGA Symposium, October 2022
  • December 13-17, 2021: AGU Fall Meeting
  • NeLLi 2021 Symposium: From New Lineages of Life to New Functions, September 16-October 21, 2021:
  • JGI Annual Genomics of Energy & Environment Meeting, August 30-September 1, 2021
  • VEGA Symposium, April 8-May 13, 2021
  • JGI Engagement Webinars
  • IMG Webinars
  • List of past User Meetings (2006 – present)
  • Microbial and Plant Systems Modulated by Secondary Metabolites Meeting, July 24-26, 2017
  • Bay Area Plant Microbe Interaction Symposium II, April 21st, 2017.
  • NeLLi: From New Lineages of Life To New Functions workshop, April 5 – 6, 2017
  • Microbial and Plant Systems Modulated by Secondary Metabolites Meeting, May 2-4, 2016
  • Plant-Microbe Interaction Symposium, April 15, 2016. Download the agenda and the poster list.
  • DOE JGI Presentations @ PAG XXIII – Download a brochure with a schedule of JGI-related presentations at the 2015 Plant & Animal Genome Meeting in San Diego, January 10-14, 2015. Or come see us along with KBase at Booth #203 in the exhibition hall.
  • 17th Genomic Standards Consortium Workshop – JGI hosted the  17th Genomic Standards Consortium (GSC 17) meeting May 4-6, 2015, followed by the satellite workshop, Genomes to Secondary Metabolites (G2SM) May 7-8, 2015.
  • Jamborees – A jamboree is a scientific meeting at which members of a scientific community gather to discuss the genome of an organism of common interest. Participants have the opportunity to annotate the genome in advance of the meeting. The focus can be a single organism or a family of organisms. Similar creatures are also typically studied in order to draw comparisons and contrasts. Attendance is by invitation.
  • 2012 Berkeley Open House Bioscriber – an educational tutorial – Developed as a means of introducing the concept of DNA synthesis/synthetic biology to the general public and how it is used at the DOE JGI and JBEI for bioenergy research, Bioscriber debuted on October 13, 2012 at the Berkeley Lab Open House. The tutorial level of this educational module shows how information from nature in the form of enzymes identified through genome sequencing can be harnessed to break down and convert plant biomass into an advanced, non-ethanol biofuel. The Bioscriber module is an ongoing project and those interested in becoming a part of the development team should contact David Gilbert, DOE JGI Public Affairs Manager. Planting & Caring for Your Poplar – An info sheet distributed with poplar seedlings that were handed out at the 2012 Berkeley Lab Open House. The poplar was the first tree to have its genome sequenced, and the work was done at the DOE JGI.
  • CSP 2012 PI Workshop
  • Science Talks at the Lesher
    – May 9, 2011,The Deal with Carbon: How Earth’s Mighty Microbes Respond. Watch on YouTube: http://bit.ly/kgaThH  – January, 18, 2011, The Future of Fuel: Local Solutions to Global Energy Challenges. Watch on YouTube: http://bit.ly/fIVE9w
  • Microbial Genome Reannotation Workshop
  • Application of High Performance Computing to the DOE Joint Genomic Institute’s Data Challenges  — January 25 – 26, 2010, Walnut Creek, CA,
  • 2022 VEGA Symposium
  • 2023 DOE Joint Genome Institute Genomics of Energy & Environment Meeting
  • MGM Workshops

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