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    Maize can produce a cocktail of antibiotics with a handful of enzymes. (Sam Fentress, CC BY-SA 2.0)
    How Maize Makes An Antibiotic Cocktail
    Zealexins are produced in every corn variety and protect maize by fending off fungal and microbial infections using surprisingly few enzymes.

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    The genome of the common fiber vase or Thelephora terrestris was among those used in the study. (Francis Martin)
    From Competition to Cooperation
    By comparing 135 fungal sequenced genomes, researchers were able to carry out a broader analysis than had ever been done before to look at how saprotrophs have transitioned to the symbiotic lifestyle.

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    Miscanthus grasses. (Roy Kaltschmidt/Berkeley Lab)
    A Grass Model to Help Improve Giant Miscanthus
    The reference genome for M. sinensis, and the associated genomic tools, allows Miscanthus to both inform and benefit from breeding programs of related candidate bioenergy feedstock crops such as sugarcane and sorghum.

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    Poplar (Populus trichocarpa and P. deltoides) grow in the Advanced Plant Phenotyping Laboratory (APPL) at Oak Ridge National Laboratory in Tennessee. Poplar is an important biofuel feedstock, and Populus trichocarpa is the first tree species to have its genome sequenced — a feat accomplished by JGI. (Image courtesy of Oak Ridge National Laboratory, U.S. Dept. of Energy)
    Podcast: Xiaohan Yang on A Plantiful Future
    Building off plant genomics collaborations between the JGI and Oak Ridge National Laboratory, Xiaohan Yang envisions customizing plants for the benefit of human society.

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    Expansin complex with cell wall in background. (Courtesy of Daniel Cosgrove)
    Synthesizing Microbial Expansins with Unusual Activities
    Expansin proteins from diverse microbes have potential uses in deconstructing lignocellulosic biomass for conversion to renewable biofuels, nanocellulosic fibers, and commodity biochemicals.

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    High oleic pennycress. (Courtesy of Ratan Chopra)
    Pennycress – A Solution for Global Food Security, Renewable Energy and Ecosystem Benefits
    Pennycress (Thlaspi arvense) is under development as a winter annual oilseed bioenergy crop. It could produce up to 3 billion gallons of seed oil annually while reducing soil erosion and fertilizer runoff.

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    Artistic interpretation of CheckV assessing virus genome sequences from environmental samples. (Rendered by Zosia Rostomian​, Berkeley Lab)
    An Automated Tool for Assessing Virus Data Quality
    CheckV can be broadly utilized by the research community to gauge virus data quality and will help researchers to follow best practices and guidelines for providing the minimum amount of information for an uncultivated virus genome.

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    Unicellular algae in the Chlorella genus, magnified 1300x. (Andrei Savitsky)
    A One-Stop Shop for Analyzing Algal Genomes
    The PhycoCosm data portal is an interactive browser that allows algal scientists and enthusiasts to look deep into more than 100 algal genomes, compare them, and visualize supporting experimental data.

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    Artistic interpretation of how microbial genome sequences from the GEM catalog can help fill in gaps of knowledge about the microbes that play key roles in the Earth's microbiomes. (Rendered by Zosia Rostomian​, Berkeley Lab)
    Podcast: A Primer on Genome Mining
    In Natural Prodcast: the basics of genome mining, and how JGI researchers conducted it in IMG/ABC on thousands of metagenome-derived genomes for a Nature Biotechnology paper.

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    Scanning electron micrographs of diverse diatoms. (Credits: Diana Sarno, Marina Montresor, Nicole Poulsen, Gerhard Dieckmann)
    Learn About the Approved 2021 Large-Scale CSP Proposals
    A total of 27 proposals have been approved through JGI's annual Community Science Program (CSP) call. For the first time, 63 percent of the accepted proposals come from researchers who have not previously been a principal investigator on an approved JGI proposal.

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    MiddleGaylor Michael Beman UC Merced
    How to Successfully Apply for a CSP Proposal
    Reach out to JGI staff for feedback before submitting a proposal. Be sure to describe in detail what you will do with the data.

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    Click on the image or go here to watch the video "Enriching target populations for genomic analyses using HCR-FISH" from the journal Microbiome describing the research.
    How to Target a Microbial Needle within a Community Haystack
    Enabled by the JGI’s Emerging Technologies Opportunity Program, researchers have developed, tested and deployed a pipeline to first target cells from communities of uncultivated microbes, and then efficiently retrieve and characterize their genomes.

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    Artistic interpretation of how microbial genome sequences from the GEM catalog can help fill in gaps of knowledge about the microbes that play key roles in the Earth's microbiomes. (Rendered by Zosia Rostomian​, Berkeley Lab)
    Uncovering Novel Genomes from Earth’s Microbiomes
    A public repository of 52,515 microbial draft genomes generated from environmental samples around the world, expanding the known diversity of bacteria and archaea by 44%, is now available .

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    Green millet (Setaria viridis) plant collected in the wild. (Courtesy of the Kellogg lab)
    Shattering Expectations: Novel Seed Dispersal Gene Found in Green Millet
    In Nature Biotechnology, a very high quality reference Setaria viridis genome was sequenced, and for the first time in wild populations, a gene related to seed dispersal was identified.

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    The Brachypodium distachyon-B. stacei-B. hybridum polyploid model complex. (Illustrations credits: Juan Luis Castillo)
    The More the Merrier: Making the Case for Plant Pan-genomes
    Crop breeders have harnessed polyploidy to increase fruit and flower size, and confer stress tolerance traits. Using a Brachypodium model system, researchers have sought to learn the origins, evolution and development of plant polyploids. The work recently appeared in Nature Communications.

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News & Publications
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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]

May 14, 2019

JGI Early Career Researchers Featured in mSystems Special Issue

Left to Right: Rex Malmstrom, Emiley Eloe-Fadrosh, and Simon Roux.In a special issue of mSystems, out May 14, 2019, JGI researchers are among the authors who offer perspectives on what the next five years of innovation could look like. In one article, Micro-Scale Applications head Rex Malmstrom and Metagenome Program head Emiley Eloe-Fadrosh outline more targeted approaches to reconstruct individual microbes in an environmental… [Read More]

April 29, 2019

Graduate Students Get Thesis Research Opportunity at the JGI

Kaze and Rambo SCGSR recipients 2018 solicitation 2 cycleTwice a year, the DOE Office of Science Graduate Student Research (SCGSR) program awards graduate students the opportunity to pursue part of their thesis research at one of the DOE national laboratories or national user facilities. As a result of the latest call, a total of 70 graduate students from 52 universities were selected to… [Read More]

April 17, 2019

Notes on the Microbial Diversity of Puerto Nuevo’s Coastline

w Sabah-Zhong_posters_UM13Puerto Nuevo is a small town along the Baja California coastline in Mexico. While conducting early field studies related to her thesis on cone snails, UC Merced graduate student Sabah Ul-Hasan and alumnus of the JGI-UC Merced Genomics Internship Program, first sampled the area in summer 2016.  She described the microbial diversity patterns of Puerto… [Read More]
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