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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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April 23, 2020

How to Target a Microbial Needle within a Community Haystack

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.A team developed a pipeline to first target cells from uncultivated microbes, and then retrieve and characterize their genomes. [Read More]

April 17, 2020

The Surprising Structure of a Shrub Willow Sex Chromosome

Female S. purpurea flowers. (Larry Smart, Cornell University)Understanding the mechanisms by which potential biofuel feedstocks reproduce can help guide breeding efforts. [Read More]

April 8, 2020

How Filamentous Fungi Sense Food

The filamentous fungus Neurospora crassa eating plant biomass. (Vincent Wu)A team led by researchers at the University of California, Berkeley used a multi-omics approach to reconstruct and model gene regulatory pathways used by the filamentous fungus Neurospora crassa, and to identify and decide on the order in which this fungus breaks down plant cell wall materials including lignin, cellulose and hemicellulose. [Read More]

February 10, 2020

Viruses Reprogram Cells into Different Virocells

How a cell behaves as virocell largely depends on the infecting virus and the genomic similarity between host and virus. Pseudoalteromonas was infected with two unrelated viruses: siphovirus PSA-HS2 and podovirus PSA-HP1. The infections transformed the same bacterial host into two very different virocells, HS2-virocell and HP1-virocell. The HS2 siphovirus genome was much more similar to the host than the genome of HP1 podovirus and had better access to recycle existing host resources. In contrast, the HP1 podovirus needed to work harder at obtaining the resources needed for infection, and reprogrammed multiple host metabolisms. HS2 virocells had a comparatively higher fitness than HP1 virocells. (Figure by Cristina Howard-Varona)If it looks like a duck and quacks like a duck, so the adage goes, it must be a duck. But if the duck gets infected by a virus so that it no longer looks or quacks like one, is it still a duck? For a team led by researchers from The Ohio State University and the University of Michigan studying how virus infections cause significant metabolic changes in marine microbes, the answer is no. They refer to the infected microbial cells as virocells, a change in name which reflects the metabolic changes they’ve undergone. [Read More]

December 20, 2019

Fishing for Novel Cellulose Degraders

Graphical representation of the cellulose hook approach. (Devin Doud)A “bait and hook” single-cell genomic approach to bioprospecting. The Science One of the most vital pieces of equipment for fly fishing is a boxful of lures. Designed with feathers or wires to mimic an insect or a particular movement, each of these lures are the bait designed to attract specific catches. A similar technique… [Read More]

December 2, 2019

Dealing with Drought: Uncovering Sorghum’s Secrets

Sorghum variety BTx642 grown in Central Valley at temperatures around 100 degrees for 65 days without water. It is still green and filling grain to almost the same extent as plants that were watered weekly. (Jeffrey Dahlberg, UC ANR Agricultural Research and Extension Center)Over 40 percent of the cereal crop’s genes respond to drought stress. The Science Fields of drooping stalks and cracked earth are becoming common images in many regions due to more extreme weather events such as heat waves, droughts and floods. The planet’s resources are being stretched by a growing human population and increasing demand… [Read More]

November 20, 2019

Making a Lichen Together

The lichen Gray’s Cup (Cladonia grayi), with its namesake goblet structures. (Thomas Barlow)For the first time, a team analyzes the transcriptomes of a lichen fungus and alga to understand their partnership more clearly. The Science The humble lichen is a superorganism: one being that is actually comprised of two (or more) participants. One is a fungus (usually belonging to the ascomycetes, one of the two main branches… [Read More]

August 20, 2019

Fungus Fuels Tree Growth

Poplar cuttings inoculated with M. elongata strain PM193 (far right) grow larger in 30 percent forest soil / 70 percent sand than without PM193 (middle). On the left are controls grown in sterile sand. (Chih-Ming Hsu)Researchers start pinning down how a fungal symbiont spurs growth of poplar, a potential biofuel feedstock.  The Science The fungus Mortierella elongata enjoys a dual lifestyle; it can thrive in the soil as a saprophyte, living off decaying organic matter, or as an endophyte, living between a plant’s root cells. The fungus is almost always… [Read More]

July 15, 2019

Better Genome Editing for Bioenergy

The lipid producing yeast, Yarrowia lipolytica, examined with light microscopy (left) and fluorescence microscopy (right), after being stained with Nile Red to visualize the lipid droplets inside (shown here in white). (Courtesy of Hal Alper)A team has optimized a crucial part of CRISPR-Cas9 technology to enable improvements in microbial oil production. The Science CRISPR-Cas9 is a powerful, high-throughput gene-editing tool that can help scientists engineer organisms for bioenergy applications. Cas9 needs guide RNA to lead it to the correct sequence to snip — but not all guides are effective…. [Read More]

July 10, 2019

Cultivating Symbiotic Antarctic Microbes

FISH of Nha-C enrichment with Hrr. lacusprofundi ACAM34-hmgA. Fluorescence micrograph shows individual Nha-C cells amongst Hrr. lacusprofundi cells. Nha-C cells labelled with a Cy5 (red fluorescence) conjugated probe; Hrr. lacusprofundi cells labelled with a Cy3 (yellow fluorescence, recolored to green to improve contrast) probe; all nucleic-acid containing cells stained with DAPI (blue fluorescence). Composite image of all three filters. Scale bars represent 2 µm. (Josh Hamm, UNSW)Nanohaloarchaeota cultures reveal they are symbionts and not free-living organisms. The Science Researchers employed multiple microbiology and ‘omics techniques to experimentally determine that Nanohaloarchaeota are symbionts, rather than free-living organisms as had been originally thought. The Impact The Antarctic lakes are a “treasure trove” of unknown microbes that play critical roles in environmental processes (related… [Read More]
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