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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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News & Publications
Home › News Releases
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April 30, 2007

Puzzling Plankton Yield Secrets to Role in Evolution/Global Photosynthesis

WALNUT CREEK, CA–The analysis of DNA sequences from tiny green algae have provided new insights into the mystery of how new species of plankton evolve–and further highlights their critical role in managing the global cycling of carbon. These findings, by a group led by the DOE Joint Genome Institute (DOE JGI); the Scripps Institution of… [Read More]

March 22, 2007

No Pain, DOE Joint Genome Institute Gains Coveted Ergonomics Prize with “Shake ‘N Plate”

WALNUT CREEK, CA–Emerging from a record field of 28 finalists representing many major multinational companies, a team of scientists and engineers from the U.S. Department of Energy Joint Genome Institute (DOE JGI) and Lawrence Berkeley National Laboratory (LBNL) won the 2007 Ergo Cup. DOE JGI’s “Shake ‘N Plate” instrument took the prize for the “team-driven… [Read More]

March 15, 2007

DOE JGI Releases Enhanced Genome Data Management System, IMG 2.1, Marking Two-Year Anniversary

WALNUT CREEK, CA–As interest in the rising number of newly characterized microbial genomes mounts, powerful computational tools become critical for the management and analysis of these data to enable strategies for such challenges as harvesting the potential of carbon-neutral bioenergy sources and coping with global climate change. The Integrated Microbial Genomes (IMG) data management system… [Read More]

March 5, 2007

Super-Fermenting Fungus Genome Sequenced

WALNUT CREEK, CA–On the road to making biofuels more economically competitive with fossil fuels, there are significant potholes to negotiate. For cellulosic ethanol production, one major detour has being addressed with the characterization of the genetic blueprint of the fungus Pichia stipitis, by the U.S. Department of Energy Joint Genome Institute (DOE JGI) and collaborators… [Read More]

January 22, 2007

DOE JGI Upgrades IMG/M, the Metagenomics Data Management & Analysis System

WALNUT CREEK, CA–On the one-year anniversary of the launch of the experimental metagenome data management and analysis system, IMG/M, the U.S. Department of Energy Joint Genome Institute (DOE JGI) has released the latest upgrade. Targeting DOE JGI’s expanding user base, IMG/M provides tools for analyzing the functional capability of microbial communities based on their metagenome… [Read More]

December 1, 2006

DOE JGI Releases IMG 2.0 with all Genomes Refreshed from RefSeq

WALNUT CREEK, CA–Version 2.0 of the Integrated Microbial Genomes (IMG) data management system of the U.S. Department of Energy Joint Genome Institute (DOE JGI) has been released to the public. The content of IMG 2.0 has been entirely refreshed and extended with the latest versions of genomes available from the National Center for Biotechnology Information’s… [Read More]

October 17, 2006

Genomic Comparison of Lactic Acid Bacteria Published

WALNUT CREEK, CA–With public concerns at a fevered pitch over the bacterial contamination of spinach, it is easy to lose track of how bland and deprived our world would be without the contribution to our food supply of such benign microbial players as lactic acid-producing bacteria. Researchers from the U.S. Department of Energy Joint Genome… [Read More]

September 26, 2006

Better Sludge through Metagenomics

WALNUT CREEK, CA–Few stop to consider the consequences of their daily ablutions, the washing of clothes, the watering of lawns, and the flush of a toilet. However, wastewater treatment–one of the corner stones of modern civilization–is the largest microbially mediated biotechnology process on the planet. When it works, it is a microbial symphony in tune… [Read More]

September 18, 2006

No Guts, No Worries: Worm Enlists Full-Service Microbes for Transportation, Energy, & Waste Management

WALNUT CREEK, CA–Researchers have now characterized the unique lifestyle of a gutless worm that commutes through marine sediments powered by a community of symbiotic microbial specialists harbored just under its skin, obviating the need for digestive and excretory systems. From a species of marine oligochaete worm isolated off of the coast of Elba, the Mediterranean… [Read More]

September 14, 2006

The First Tree Genome is Published

poplar on Science 2006 coverIn Science, the first complete DNA sequence of a tree – the black cottonwood or Populus trichocarpa – lays the groundwork that may lead to feedstock for a new generation of biofuels. [Read More]
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