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    A vertical tree stump outdoors with about a dozen shiitake mushrooms sprouting from its surface.
    Tracing the Evolution of Shiitake Mushrooms
    Understanding Lentinula genomes and their evolution could provide strategies for converting plant waste into sugars for biofuel production. Additionally, these fungi play a role in the global carbon cycle.

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    Soil Virus Offers Insight into Maintaining Microorganisms
    Through a collaborative effort, researchers have identified a protein in soil viruses that may promote soil health.

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    Data yielded from RIViT-seq increased the number of sigma factor-gene pairs confirmed in Streptomyces coelicolor from 209 to 399. Here, grey arrows denote previously known regulation and red arrows are regulation identified by RIViT-seq; orange nodes mark sigma factors while gray nodes mark other genes. (Otani, H., Mouncey, N.J. Nat Commun 13, 3502 (2022). https://doi.org/10.1038/s41467-022-31191-w)
    Streamlining Regulon Identification in Bacteria
    Regulons are a group of genes that can be turned on or off by the same regulatory protein. RIViT-seq technology could speed up associating transcription factors with their target genes.

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    The switchgrass diversity panel growing at the Kellogg Biological Station in Michigan. (David Lowry)
    Mapping Switchgrass Traits with Common Gardens
    The combination of field data and genetic information has allowed researchers to associate climate adaptations with switchgrass biology.

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    Artist rendering of genome standards being applied to deciphering the extensive diversity of viruses. (Illustration by Leah Pantea)
    Expanding Metagenomics to Capture Viral Diversity
    Along with highlighting the viruses in a given sample, metagenomics shed light on another key aspect of viruses in the environment — their sheer genetic diversity.

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    Photograph of a stream of diatoms beneath Arctic sea ice.
    Polar Phytoplankton Need Zinc to Cope with the Cold
    As part of a long-term collaboration with the JGI Algal Program, researchers studying function and activity of phytoplankton genes in polar waters have found that these algae rely on dissolved zinc to photosynthesize.

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    Silver Age of GOLD Introduces New Features
    The Genomes OnLine Database makes curated microbiome metadata that follows community standards freely available and enables large-scale comparative genomics analysis initiatives.

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    Graphical overview of the RNA Virus MetaTranscriptomes Project. (Courtesy of Simon Roux)
    A Better Way to Find RNA Virus Needles in the Proverbial Database Haystacks
    Researchers combed through more than 5,000 data sets of RNA sequences generated from diverse environmental samples around the world, resulting in a five-fold increase of RNA virus diversity.

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    HPCwire Editor's Choice Award (logo crop) for Best Use of HPC in the Life Sciences
    JGI Part of Berkeley Lab Team Awarded Best Use of HPC in Life Sciences
    The HPCwire Editors Choice Award for Best Use of HPC in Life Sciences went to the Berkeley Lab team comprised of JGI and ExaBiome Project team, supported by the DOE Exascale Computing Project for MetaHipMer, an end-to-end genome assembler that supports “an unprecedented assembly of environmental microbiomes.”

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    Digital ID card with six headshots reads: Congratulations to our 2022 Function Genomics recipients!
    Final Round of 2022 CSP Functional Genomics Awardees
    Meet the final six researchers whose proposals were selected for the 2022 Community Science Program Functional Genomics call.

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    CSP New Investigators FY23 R1
    JGI Announces First Round of 2023 New Investigator Awardees
    Twice each year we look for novel research projects aligned with DOE missions and from PIs who have not led any previously-accepted proposals through the CSP New Investigator call.

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    screencap from Amundson and Wilkins subsurface microbiome video
    Digging into Microbial Ecosystems Deep Underground
    JGI users and microbiome researchers at Colorado State University have many questions about the microbial communities deep underground, including the role viral infection may play in other natural ecosystems.

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    2022 JGI-UC Merced interns (Thor Swift/Berkeley Lab)
    Exploring Possibilities: 2022 JGI-UC Merced Interns
    The 2022 UC Merced intern cohort share how their summer internship experiences have influenced their careers in science.

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    Using Team Science to Build Communities Around Data
    As the data portals grow and evolve, the research communities further expand around them. But with two projects, communities are forming to generate high quality genomes to benefit researchers.

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    Cow Rumen and the Early Days of Metagenomics
    Tracing a cow rumen dataset from the lab to material for a hands-on undergraduate research course at CSU-San Marcos that has since expanded into three other universities.

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Home › Items tagged with: agriculture

Content Tagged "agriculture"

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December 3, 2012

DOE JGI partners Cornell on cassava project

Cassava, a rough and ready root crop that has long been the foundation of food security in Africa is finally getting the respect it deserves. The Bill & Melinda Gates Foundation and the Department for International Development of the United Kingdom (DFID) are investing $25.2 million to improve the staple crop’s productivity and build human… [Read More]

August 3, 2012

Arabidopsis root microbiome project: release from University of Queensland

Led by the University of North Carolina and the US Department of Energy Joint Genome Institute, the research studied the microbiome in soil around the roots of more than 600 Arabidopsis thaliana plants. The team, which included The University of Queensland Professor Philip Hugenholtz, investigated how the microbiome helps shuttle nutrients and information into and out… [Read More]

June 1, 2012

Comparative genomics method to tag novel nitrogen-fixation genes

Nitrogen is crucial for plant growth but plants cannot harness it directly from the atmosphere. In the United States, legume crops such as soybeans and peas rely on nitrogen fertilizers to boost yields; in 2007, 13 million tons of industrially-produced fertilizers were applied. Soil bacteria such as Sinorhizobiummeliloti have a symbiotic relationship with plant hosts… [Read More]

April 13, 2012

An alternative surrogate for gene discovery in switchgrass

Selected for the DOE JGI 2007 Community Sequencing Program because of traits such as high yield, perennial growth and low nutrient requirements, switchgrass is a promising candidate bioenergy crop that could be used to develop cellulosic biofuels. One of the challenges with sequencing switchgrass is the fact that it is a polyploid, containing multiple, full… [Read More]

January 7, 2012

Cotton project in the Delta Farm Press

An international consortium, led by Professor Andrew Paterson of the University of Georgia, has made publicly available the first ‘gold-standard’ genome sequence for cotton. Cotton was among the first plants studied at the molecular level, and the sequence obtained by Paterson and his team is the culmination of a 20-plus year effort in the analysis… [Read More]

December 9, 2011

Boosting knowledge of nitrogen-fixing bacteria

No plant is an island; interactions with complex microbial communities both above the ground and below the ground shape the plant’s growth rates and overall health. Understanding these plant-microbe interactions can lead to improvements in plant health and productivity and carbon sequestration, which can be applied toward DOE missions in bioenergy and biogeochemistry. Dark-field photo… [Read More]

November 28, 2011

Spider mite genome project in CBC News

“They can change the repertoire [of genes] that they’re using in order to be able to feed on hosts that they would not be adapted to,” said Miodrag Grbic, a University of Western Ontario biologist, who led an international project to sequence the spider mite’s genome. The results were published this week in the journal… [Read More]

November 23, 2011

Spider mite genome project in GenomeWeb

The spider mite, named for its ability to spin webs, belongs to an arthropod sub-group comprised of so-called chelicerates and is capable of consuming more than 1,100 plant species. This trait, coupled with its ability to develop resistance to most commonly used pesticides, have made it a potent pest, known for damaging ornamental plants and… [Read More]

July 19, 2011

Dry rot (Serpula) genome project on eNews Park Forest

In 2007 the US Department of Energy’s Joint Genome Institute sequenced Serpula lacrymans in order to see if the way it breaks down cellulose in wood could be harnessed for biofuel production. An international team analysing the genome have found the enzyme mechanisms that could explain the aggressive decay caused by this form of dry… [Read More]

June 17, 2011

Cassava project in Bloomberg View

Over the past few years, the U.S. Department of Energy’s Joint Genome Institute has taken up the challenge to sequence additional starches that could make a significant difference in developing nations where corn and soybean are less important than such staples as foxtail millet, sorghum and cassava. Such crops, if engineered to be more nutritious,… [Read More]
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