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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
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November 16, 2021

JGI Part of Berkeley Lab Team Awarded Best Use of HPC in Life Sciences

HPCwire Editor's Choice Award (logo crop) for Best Use of HPC in the Life SciencesThe 2021 HPCwire Editors’ Choice Award for Best Use of HPC in Life Sciences goes to the JGI/ExaBiome Project/Exascale Computing Project team for MetaHipMer. [Read More]

October 26, 2021

The Case for Conservation

Female (left) and male (right) Ceratodon purpureus plants. Females typically grow larger than males in several traits, like the length of leaves. Males often turn red when developing antheridiophores, which in mosses are the structures that produce sperm (seen in the bottom right. (Sarah Carey)High-quality reference genome sequences of the male and female fire moss plants are now available, and lessons from their sex chromosomes could help improve crop yields. [Read More]

October 4, 2021

Anuvia taps JGI for expertise to pinpoint products from beneficial soil microbes

From USAID, crops grown on the farm of Davane Mesa Paulo. (Bita Rodriguez)Anuvia, a small Florida business, is partnering with the JGI to help drive discoveries that will render new economic advantages for farmers concerned with improving sustainable soil management practices. [Read More]

September 29, 2021

Promoting the Power of Viral Metagenomics

Workflow for identifying viral sequences in most common sample types, a figure from their article summarizing the field of viral metagenomics.JGI researchers summarized the field of viral metagenomics in an article for the journal Annual Review of Biomedical Data Science. [Read More]

September 24, 2021

Monitoring Inter-Organism Interactions Within Ecosystems

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)The latest portfolio of proposals approved through the JGI’s annual Community Science Program (CSP) call. [Read More]

September 22, 2021

Plotting a Model for Virus-Host Warfare Deep Below Ground

Image of biofilm with both Altiarchaea (blue) and viruses (red). (Victoria Turzynksi and Lea Griesdorn)Researchers describe how viruses repeatedly attempt to infect and destroy their hosts – and how the microbes resist. [Read More]

September 16, 2021

Climate Change Threatens Base of Polar Oceans’ Bountiful Food Webs

Scientists sample a brown mat of aggregated phytoplankton. (Katrin Schmidt)A study suggests climate change is behind a trend that could destabilize the delicate marine food web. [Read More]

August 27, 2021

Boosting Small Molecule Production in Super “Soup”

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)Researchers describe a two-pronged approach that starts with engineered yeast cells but then moves out of the cell structure into a cell-free system. [Read More]

August 26, 2021

Virus-Microbe Interactions of Mud Island Mangroves

Ian Rambo, graduate student at UT-Austin, was a DOE Graduate Student Research Fellow at the JGIIan Rambo conducted part of his graduate work at the JGI through the DOE Office of Science Graduate Student Research (SCGSR) program. [Read More]

August 2, 2021

Designer DNA: JGI Helps Users Blaze New Biosynthetic Pathways

(PXFuel)A special issue of Synthetic Biology celebrates research enabled by the JGI DNA Synthesis Science Program. [Read More]
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