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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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Our Science
Home › Science Highlights
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May 30, 2018

DAS Tool for Genome Reconstruction from Metagenomes

The Angelo Coast Range Reserve, from which soil samples were taken, protects thousands of acres of the upper watershed of South Fork of the Eel River (shown here) in Mendocino County. (Akos Kokai via Flickr, CC BY 2.0 https://www.flickr.com/photos/on_earth/17307333828/)Developing and validating an integrated approach to genome recovery from metagenomes. The Science Through the JGI’s Emerging Technologies Opportunity Program (ETOP), researchers have developed and improved upon a tool that combines existing DNA sequence binning algorithms, allowing them to reconstruct more near-complete genomes from soil metagenomes compared to other methods. The Impact Understanding how individual… [Read More]

May 23, 2018

Iron-rich Microbial Mats’ Main Players: Marsarchaeota

The iron (Fe)-oxide terraces at Echinus Geyser form from the oxidation of ferrous Fe, and the temperature across the terraces ranges from ~ 60-70ºC, while pH values vary from 3.4 to 3.6. A very thin (1-2 mm) layer of water flowing over the Fe-oxide terraces from the outflow channel at Echinus Geyser, located in Yellowstone National Park’s Norris Geyser Basin, is thought to provide the needed oxygen to create habitats suitable for the Marsarchaeota. (Bill Inskeep)Novel archaeal lineage found in Yellowstone may have been important in early Earth conditions. The Science Through a combination of sequencing tools and techniques applied to samples collected from acidic iron-oxide microbial mats in Yellowstone National Park over time, researchers have discovered and characterized a novel phylum-level lineage of archaea with at least two major… [Read More]

January 8, 2018

The fungus that made itself at home

Serpula lacrymans var shastensis decomposing a large Shasta red fir (Abies magnifica var shastenis) in its natural habitat in Mt Shasta, California. (Håvard Kauserud)Retracing how the dry rot Serpula lacrymans adapted to a new ecological habitat. The Science By comparing genetic information from similar organisms, researchers have gained insights on why the dry rot (Serpula lacrymans) is so destructive in houses. A study involving six brown rot fungi reveals the genomic changes Serpula lacrymans has undergone in adapting… [Read More]

December 13, 2017

An Addiction Crucial to a Fungus’ Reproduction

Sexual reproduction in Rhizopus microspores: (a) Successful mating between fungi harboring bacteria; (b) Lack of sex between mates cured of endobacteria. (Stephen Mondo)A fungus relies on bacteria to regulate key components of its reproductive machinery The Science To better understand how beneficial organisms (symbionts) are transmitted between host generations, researchers investigated the role that bacteria living within a host (endosymbionts) have on fungal host reproduction, and the reproductive genes they regulate. The bacterial endosymbiont, Burkholderia, is recognized… [Read More]

December 1, 2017

Succulent Genes for Water Use Efficiency

In Nature Communications, researchers sequenced and analyzed the genome of Kalanchoe fedtschenkoi (lavender scallops) to better understand how this plant transitioned from C3 to CAM photosynthesis. (Forest and Kim Starr, Flickr CC BY 2.0)Comparative genomics identifies sequences involved in photosynthesis under reduced water conditions.   The Science In the presence of sufficient water and light, most plants conduct photosynthesis through what is known as the C3 pathway. As plants spread out and adapted to live in a variety of environments, they developed alternate photosynthesis pathways, known as C4 and… [Read More]

November 24, 2017

Insights into carbon fixation in the dark ocean  

View of Saanich Inlet - one of the areas sampled for this study - from Malahat. (BC Ministry of Transportation, Flickr CC BY-NC-ND 2.0)Nitrite-oxidizing bacteria have bigger role in marine carbon cycle than previously thought The Science Researchers have identified the most abundant and globally distributed nitrite-oxidizing bacteria (NOB) in the oceans, through single-cell genomics and community meta-omics. They have also calculated the NOB’s contribution toward trapping carbon beneath the sunlit waters and determined that though these bacteria… [Read More]

October 4, 2017

A Technique for Targeted Improvement

A bioluminescent assay helped researchers visually quantify the colonization ability of P. simiae mutant strains identified by the RB-TnSeq screen. (Benjamin Cole)Establishing a genome-wide map of bacterial genes crucial for colonization of plants by beneficial microbes The Science Working with the plant growth-promoting bacterium Pseudomonas simiae, researchers have identified 115 genes that negatively affect its ability to colonize a plant root system when mutated. The Impact A plant’s health and development is influenced by the complex… [Read More]

September 5, 2017

Scaling Microbial Genomics Discoveries for Ecosystem Modeling

Study co-author Rhonzhong Ye and graduate student Jennifer Morris collecting greenhouse gas fluxes from the rice fields studied on Twitchell Island, CA. (Wyatt Hartman)Nutrient availability in model wetlands helps regulate microbial metabolism and soil carbon cycling rates The Science Studying microbial communities in San Joaquin Delta rice fields, researchers linked microbial metabolism and nutrient availability to soil carbon cycling rates. The Impact Establishing the inter-relationships among microbial metabolism, nutrient availability and soil carbon cycling rates is critical to… [Read More]

July 31, 2017

Tracking Microbial Succession in Petroleum Wells

Shell researchers collected samples from oil wells in a North Sea oil field like this one. (Credit: Berardo62 via Flickr CC BY-SA 2.0)Offshore subsurface reservoirs demonstrate human impacts on well microbiomes. The Science Microbes are invisible to the naked eye, but play key roles in maintaining the planet’s biogeochemical cycles. In the Earth’s subsurface, microbes have adapted to thrive in the relatively stable extreme conditions. To learn more about how some of these populations respond to disruptions… [Read More]

July 19, 2017

Insights into A Eukaryotic Alga

Porphyra umbilicalis (laver) attains high biomass despite the high levels of stress in its habitat in the upper intertidal zone of the North Atlantic, as shown here at low tide at Sand Beach, Acadia National Park, Maine. (Susan Brawley)The genome of Porphyra umbilicalis reveals the mechanisms by which it thrives in the intertidal zone The Science Through the Community Science Program of the U.S. Department of Energy Joint Genome Institute (DOE JGI), a DOE Office of Science User Facility, a 50-member team led by University of Maine, Carnegie Institution for Science, and East… [Read More]
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