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    Screencap of green algae video for PNAS paper
    Green Algae Reveal One mRNA Encodes Many Proteins
    A team of researchers has found numerous examples of polycistronic expression – in which two or more genes are encoded on a single molecule of mRNA – in two species of green algae.

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    Advances in Rapidly Engineering Non-model Bacteria
    CRAGE is a technique for chassis (or strain)-independent recombinase-assisted genome engineering, allowing scientists to conduct genome-wide screens and explore biosynthetic pathways. Now, CRAGE is being applied to other synthetic biology problems.

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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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    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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    Image of Octopus Springs for the CSP annual call
    Letters of Intent are due April 12, 2021 for the annual Community Science Program (CSP) call focused on large-scale genomic science projects that address specific areas of special emphasis and exploit the diversity of JGI capabilities.

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    SIP engagement webinar
    “SIP technologies at EMSL and JGI” Webinar
    The concerted stable isotope-related tools and resources of the JGI and the Environmental Molecular Sciences Laboratory (EMSL) may be requested by applying for the annual “Facilities Integrating Collaborations for User Science” (FICUS) call.

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    CSP Functional Genomics Call Ongoing
    The CSP Functional Genomics call helps users translate genomic information into biological function. Proposals submitted by July 31, 2021 will be part of the next review.

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    Aerial photo of the switchgrass diversity panel late in the 2020 season at the Kellogg Biological Station in Michigan. (Robert Goodwin)
    A Team Effort Toward Targeted Crop Improvements
    A multi-institutional team has produced a high-quality reference sequence of the complex switchgrass genome. Building off this work, researchers at three DOE Bioenergy Research Centers have expanded the network of common gardens and are exploring improvements to switchgrass.

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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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News & Publications
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October 2, 2017

Benchmarking Computational Methods for Metagenomes

Table showing partial results of assemblers applied to the 1st CAMI Challenge, Dataset 1.Community-driven CAMI Challenge offers analysts, scientists insights on the right tools for their research questions. They are everywhere, but invisible to the naked eye. Microbes are the unseen, influential forces behind the regulation of key environmental processes such as the carbon cycle, yet most of them remain unknown. For more than a decade, the U.S…. [Read More]

September 26, 2017

2018 DOE JGI Community Science Program Allocations Announced

Mucor circinelloides sporangiophore. (S. Torres-Martínez. University of Murcia, Spain.)Proposals encompass multiple capabilities of the national user facility Though organisms can be studied in isolation, a more comprehensive picture emerges when their environmental interactions are taken into account. Along the same lines, many of the 30 proposals selected for the 2018 Community Science Program (CSP) of the U.S. Department of Energy Joint Genome Institute (DOE… [Read More]

August 23, 2017

DOE User Facilities Partner for Greater Scientific Impact

Phylogenetic diversity of metagenome assembled genomes (MAGs) from the Canada Basin and Beaufort SeaEMSL and DOE JGI announce FY 2018 FICUS projects Two Department of Energy user facilities, the Environmental Molecular Sciences Laboratory (EMSL) and the Joint Genome Institute (JGI), have selected 14 proposals from a joint call for 2018 research under the Facilities Integrating Collaborations for User Science (FICUS) initiative. This was the fifth FICUS call between EMSL… [Read More]

August 9, 2017

Defining Standards for Genomes from Uncultivated Microorganisms

The importance of standards is dramatically illustrated when they don’t exist or are not commonly accepted. an international team led by DOE JGI researchers has developed standards for the minimum metadata to be supplied with single amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) submitted to public databases. (Zosia Rostomian, Berkeley Lab Creative Services)Expanding minimum information standards for single-cell genomics, metagenomics datasets. During the Industrial Revolution, factories began relying on machines rather than people for mass production. Amidst the societal changes, standardization crept in, from ensuring nuts and bolts were made identically to maintain production quality, to a standard railroad gauge used on both sides of the Atlantic…. [Read More]

July 25, 2017

DOE User Facilities Join Forces to Tackle Biology’s Big Data

Users can look for patterns across data sets in the DOE JGI’s Integrated Microbial Genomes and Microbiomes (IMG/M) database with the help of NERSC’s supercomputer Cori. (Roy Kaltschmidt, Berkeley Lab)Inaugural Collaborative Science Call Yields Six Proposals Melding Genomics, Supercomputing Six proposals have been selected to participate in a new partnership between two U.S. Department of Energy (DOE) user facilities through the “Facilities Integrating Collaborations for User Science” (FICUS) initiative. The expertise and capabilities available at the DOE Joint Genome Institute (JGI) and the National… [Read More]

June 12, 2017

Uncovered: 1000 New Microbial Genomes

GEBA NatBiotech ZosiaRostomianPotential biotech applications seen with release of 1,003 reference bacterial and archaeal genomes.   The number of microbes in a handful of soil exceeds the number of stars in the Milky Way galaxy, but researchers know less about what’s on Earth because they have only recently had the tools to deeply explore what is just… [Read More]

May 26, 2017

Fungal Enzymes Team Up to More Efficiently Break Down Cellulose

Scanning electron micrograph (SEM) of Neocallimastix californiae, a representative of the Neocallimastigomycetes, a clade of the early-diverging fungal lineages that are not well-studied. It's one of three Neocallimastigomycetes sequenced and annotated by the DOE JGI for this study. (Chuck Smallwood, PNNL)Collaborative science initiative enables resolution of fungal protein complexes. One of the biggest barriers in the commercial production of sustainable biofuels is to cost-effectively break down the bioenergy crops into sugars that can then be converted into fuel. To reduce this barrier, bioenergy researchers are looking to nature and the estimated 1.5 million species of… [Read More]

May 8, 2017

Finding A New Major Gene Expression Regulator in Fungi

Linderina pennispora ZyGoLife Research Consortium Flickr CC BY-SA 2.0Researchers report prevalent DNA base modification in the earliest fungal lineages Just four letters – A, C, T, and G – make up an organism’s genetic code. Changing a single letter, or base, can lead to changes in protein structures and functions, impacting an organism’s traits. In addition, though, subtler changes can and do happen,… [Read More]

April 6, 2017

Discovered: Novel Group of Giant Viruses

Giant virus acquiring genes from different eukaryotic host cells. (Ella Maru studio, http://www.scientific-illustrations.com/)Giant viruses appear to have evolved from smaller viruses (not from cells) based on presence of nearly complete set of translation-related genes. Viruses have a ubiquitous presence in the world. Their population is estimated to be 1031, 10 times greater than the nonillion (1030) of microbes on the planet—a figure that surpasses the number of… [Read More]

February 27, 2017

Revealing Aspergillus Diversity for Industrial Applications

Comparative growth of aspergilli. (Ad Wiebenga & Ronald de Vries, Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands)Comparative analysis of Aspergillus species provides genus-wide view of fungal diversity In the world of fungi, Aspergillus is an industrial superstar. Aspergillus niger, for example, has been used for decades to produce citric acid—a compound frequently added to foods and pharmaceuticals —through fermentation at an industrial scale. Other species in this genus play critical roles… [Read More]
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