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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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June 11, 2019

Developing Switchgrass for Biomass Production

Left to Right: Jerry Jenkins, JGI Plant Program head Jeremy Schmutz, Adam Healey and study senior author Tom Juenger of UT-Austin.Switchgrass community gardens help distinguish genetic bases of fitness traits from climactic influence. The Science To better understand the genetic basis of local adaptation, researchers established community gardens of switchgrass plants in 10 different field sites on a north-south gradient across the United States. Hundreds of the switchgrass plants in these gardens are clonally propagated… [Read More]

February 25, 2019

Evolution of a Fungal Gene Expression Regulator

Parasitella parasitica (ZyGoLife Research Consortium on Flickr, CC BY-SA 2.0)Describing the largest analysis to date of the modified DNA base 5mC variations in fungi. by Massie S. Ballon The Science Changing an A, C, T or G in a genome sequence can lead to changes in protein structures and functions, but the DNA bases themselves can also be modified. The best-known example of a… [Read More]

December 7, 2018

A Model System for Perennial Grasses

Field researchers studying drought responses in Panicum hallii at the UT Austin Brackenridge Field Lab. (David Gilbert)Panicum hallii genomes offer insights to drought tolerance. The Science Researchers have developed a genomic model to study drought tolerance in perennial grasses using Panicum hallii (Hall’s panicgrass), by generating two complete genomes from varieties that diverged over a million years ago. The hallii variety thrives in desert environments, while the filipes variety is less… [Read More]

October 19, 2018

Mining Metagenomes for Cas Proteins

Click on the image above or click here (https://youtu.be/iSEEw4Vs_B4) to watch a CRISPR Whiteboard Lesson from the Innovative Genomics Institute, this one focuses on the PAM sequence.Cas14 proteins discovered from JGI’s IMG/M database and biochemically characterized at UC Berkeley and the Innovative Genomics Institute.  The Science Researchers report the discovery of miniature Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) associated proteins that can target single-stranded DNA (ssDNA). The discovery was made possible by mining the datasets in the Integrated Microbial Genomes… [Read More]

October 8, 2018

Mapping Heat Resistance in Yeasts

At high temperature, S. paradoxus cells die in the act of cell division, as seen by the dyads with cell bodies shriveled away from the outer cell wall. (Images by Carly Weiss, courtesy of the Brem Lab)A new approach for improving functional annotation in fungal genomes. The Science In a proof-of-concept study, researchers demonstrated that a new genetic mapping strategy called RH-Seq can identify genes that promote heat resistance in the brewer’s/baker’s yeast Saccharomyces cerevisiae, allowing this species to grow better than its closest relative S. paradoxus at high temperatures (39°C/102°F)…. [Read More]

September 24, 2018

First Monoploid Reference Sequence of Sugarcane

The reference sequence is useful for mapping the genes involved in sugar production and for identifying different variants on different chromosomes, information that can be used to assemble a more complex and more realistic polyploid sugarcane genome now underway. (Rufino Uribe, CC-SA 2.0)Sorghum genome serves as a reference for the highly complex sugarcane genome. The Science Most species are diploids and have two sets of chromosomes, one from each parent. In contrast, many crops have multiple sets of chromosomes (they are “polyploid”) and their complex genomes are more difficult to sequence and assemble, in turn limiting the… [Read More]

September 5, 2018

Defining a Pan-Genome for Antarctic Archaea

Antarctica’s Deep Lake. (Rick Cavicchioli)Analysis of haloarchaeal metagenomes broadens understanding of Antarctic biogeography. The Science Haloarchaea flourish in hypersaline environments, and researchers are interested in learning how these microbes have learned to adapt from marine to hypersaline conditions by studying the microbial communities in Antarctic lakes, some of which have salinities 10 times that of seawater. To shed light… [Read More]

August 13, 2018

Corymbia Genome Expands Terpene Synthesis Knowledge

Corymbia citriodora subspecies citriodora is a native of north Queensland in Australia but is grown throughout the subtropics for essential oil production. (Photo by Mervyn Shepherd)Genome annotations of two C. citriodora subspecies broaden understanding of the terpene synthase gene family across eucalypt lineages. The Science From the distinct smell of eucalyptus to the flavor of wine, terpenes are ubiquitous. A diverse group of plant-produced organic compounds, terpenes play key roles in plant growth, defense, and environmental interactions. Terpenes are also… [Read More]

July 6, 2018

Innovative Technology Improves Our Understanding of Bacterial Cell Signaling

The molecule cyclic di-GMP plays a key role in controlling cellulose production and biofilm formation. To better understand cyclic di-GMP signaling pathways, the team developed the first chemiluminescent biosensor system for cyclic di-GMP and showed that it could be used to assay cyclic di-GMP in bacterial lysates. (Image courtesy of Hammond Lab, UC Berkeley)Newly developed chemiluminescent biosensors shed light on how bacteria function and colonize diverse environments. The Science Cyclic di-GMP (Guanine Monophosphate) is found in nearly all types of bacteria and interacts with cell signaling networks that control many basic cellular functions. It plays an important role in regulating microbial cellulose production and biofilm formation, which affects… [Read More]

June 13, 2018

Building Sphagnum Genomic Resources

Sphagnum fallax (Image courtesy of Jonathan Shaw, Duke University)Sphagnome data would enable researchers’ insights on their potential carbon cycling impact. The Science Enabled by the JGI’s Community Science Program (CSP), researchers are developing a number of resources to build up Sphagnum as a plant model system focused on carbon cycling studies, rather than for food or fuel applications. The Impact Sphagnum’s impact on… [Read More]
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