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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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    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 21, 2022

JGI at 25: Cow rumen and the early days of metagenomics

The dataset from a 2011 paper identifying microbial genes in cow rumen is now used for a hands-on undergraduate research course at four universities. [Read More]

November 14, 2022

JGI at 25: Stories from Intern Alumni

Hands-on experience can be life changing for students. Hear former JGI interns share how these experiences have influenced their career journeys. [Read More]

November 3, 2022

Genome Insider S3 Episode 4: From Sample Shipments to Sequences – A Tour of the JGI’s Sequencing Pipeline

A Genome Insider Logo ImageEvery year, the JGI sequences around 35,000 samples — from plants, algae, bacteria, archaea, fungi, viruses — to support scientists around the world. Most of those researchers send their samples in from afar, without ever hearing much about the sequencing lab. So today, Chris Daum walks through the JGI’s sequencing pipeline, where there are freezers with names — but not doors — and robots handle a bunch of benchwork. [Read More]

October 19, 2022

JGI at 25: Fueling investigation into methane-making microbes

An image of Robert Hungate set against a blue background with white bacteria imagesIn 2018, the JGI helped assemble the Hungate1000 catalog. To date it is the single largest effort to provide a cataloged and curated culture and genome sequence resource of rumen microorganisms.  [Read More]

October 3, 2022

RECAP: 2022 Annual Meeting features historical perspectives on JGI’s 25 years

A man stands at a podium with a mural in the backgroundAs part of the JGI’s 25th anniversary celebration, the 2022 Annual Meeting featured speakers whose talks shed light on how the JGI was established, all that it has contributed, and what they’re excited about in JGI’s future. [Read More]

October 3, 2022

RECAP: Keynote Speakers Talk Innovation at 2022 JGI Annual Meeting

A woman presents virtually, visible from a large projector screen before her audienceThe JGI hosted some of the brightest minds in genetics as part of our 2022 Annual Meeting: Nobel Laureate Jennifer Doudna of UC Berkeley and Berkeley Lab, Assaf Vardi of the Weizmann Institute of Science, and Susan Wessler of UC Riverside. [Read More]

September 26, 2022

JGI at 25: Strengthening Soybean

A white bowl of beige soybeans is set against a black background. On top of the individual beans is a pea pod.Maximizing soybean yield is critical to energy independence in the U.S. Not only does it pair with maize, the dominant source of bioethanol, in crop rotation, but soybean (Glycine max) also has the advantage of reducing the need for nitrogen fertilizer. These impressive environmental and energy advantages explain why soybean is a flagship genome of the JGI’s Plant Program.   [Read More]

August 11, 2022

JGI at 25: The Little Alga That Could

Chlamydomonas is an insightful little alga that holds clues to leveraging other organisms for sustainable biofuel production. [Image: MPI-CBG, Dresden]Since the JGI’s sequencing of Chlamydomonas reinhardtii — the tiny alga with a mighty impact — became available, those sequences have been cited in almost one-fourth (23.8%) of publications focused on that specific algae. The reference genome is cited in roughly 10% of all since-released publications on green algae. [Read More]

July 11, 2022

JGI at 25: Building a Better Bean

The common bean (Phaseolus vulgaris) includes pinto beans, kidney beans, black beans, navy beans and more. (Image Credit: TK)The JGI’s original reference genome for Phaseolus vulgaris has been instrumental in creating a hardier, higher-yield bean. [Read More]

July 1, 2022

Supporting Global Research into Actinomycetes

StreptomycesActinoBase, a public platform built on the knowledge of researchers studying actinomycetes, is the focus of a recent paper published in Microbial Genomics, ”ActinoBase: An Actinomycete Community Wiki.” [Read More]
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