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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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September 18, 2019

Meet a JGI Postdoc: Ritesh Mewalal

NPAW 2019 JGI postdoc Ritesh MewalalFrom September 16-20, 2019, we introduce you to some of the postdocs at the JGI in honor of National Postdoc Appreciation Week, which recognizes the contributions of these early career researchers. Through a series of hard-hitting questions, we find out what drives each one.   What are you working on? Beneficial plant-microbe interactions alter valuable… [Read More]

September 17, 2019

Meet a JGI Postdoc: Kyle Hartman

NPAW 2019 JGI postdoc Kyle HartmanFrom September 16-20, 2019, we introduce you to some of the postdocs at the JGI in honor of National Postdoc Appreciation Week, which recognizes the contributions of these early career researchers. Through a series of hard-hitting questions, we find out what drives each one.   What are you working on? I am a member of the… [Read More]

September 16, 2019

Meet a JGI Postdoc: Sara Calhoun

NPAW 2019 JGI postdoc Sara CalhounFrom September 16-20, 2019, we introduce you to some of the postdocs at the JGI in honor of National Postdoc Appreciation Week, which recognizes the contributions of these early career researchers. Through a series of hard-hitting questions, we find out what drives each one.   What are you working on? I have two main projects:… [Read More]

September 6, 2019

Scaling Up Existing Skill Sets

2019 JGI-UC Merced internship programOver the course of the summer, the JGI-UC Merced Genomics Internship paired six UC Merced students with seven JGI researchers for bioinformatics internship opportunities in fields ranging from plant-microbe interactions to functional genomics. Hear from five of the Summer 2019 interns, who briefly shared their experiences below.   Name: Noelle Anderson Class Year: At the… [Read More]

August 30, 2019

Game On: High School Students Drive Everglades Metagenomics Study

In late June, Kathleen Lail, a member of JGI’s Sample Management Group, attended a conference in Florida to discuss a JGI pilot project involving soil sampling in the Florida Everglades to help train the next generation of scientists. She shares her thoughts about the experience below. In the summer of 2018, Jonathan Benskin was preparing… [Read More]

August 14, 2019

Panel Discussion: Launching & Sustaining Startups in Synthetic Biology

The Berkeley Lab Biosciences Area Entrepreneurship Program presents… Eyes on the Prize – Launching & Sustaining Startups in Synthetic Biology Who’s Invited? All Berkeley Lab Employees and Affiliates. When: August 29th, 3:00 pm – 5:30 pm 3:00 pm – 4:15 pm: Panel discussion, Q&A followed by: 4:15 pm – 5:30 pm: Hosted Hoppy Hour @… [Read More]

July 23, 2019

JGI User Executive Committee charter

The JGI User Executive Committee (UEC) represents the JGI user community and is responsible for providing input and advice on JGI policies and practices that affect users and their science including technical capabilities offered, proposal review procedures, and the annual user meeting.  The UEC also acts as a liaison to the user community and the… [Read More]

July 19, 2019

Improving the Cacao Genome and Phytozome

According to the International Cocoa Organization (ICCO), global cocoa bean production in 2017-2018 was 4.6 million metric tons. The global chocolate brands couldn’t exist without cocoa.  But today the plant is under threat due to climate change and devastating fungal infections. That’s why Mars, Inc., a maker of chocolate for more than 100 years and… [Read More]

June 10, 2019

Tracking Permafrost Thaw

Virginia Rich, Ohio State, at the JGI 2019 User MeetingNotes from the JGI 2019 User Meeting The Arctic peatlands are among the northern ecosystems that collectively store up to half of the planet’s soil carbon. With the frozen peatlands thawing, said Virginia Rich of The Ohio State University, “if we project this out, permafrost is virtually eliminated by the end of the century.” Just… [Read More]

June 7, 2019

Engaging the Workforce through Tiny Earth

Amanda Hurley of the University of Wisconsin–Madison at the JGI 2019 User MeetingNotes from the JGI 2019 User Meeting Amanda Hurley, a postdoctoral fellow in Jo Handelsman’s lab at the University of Wisconsin–Madison, began her talk with a reminder that pathogens damage 16% of the global crop yield. That number is expected to rise due to climate change. “We need something that tips the scales back in… [Read More]
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