DOE Joint Genome Institute

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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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All JGI Features
Home › Items tagged with: USDA

Content Tagged "USDA"

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October 12, 2011

Director Rubin on corngrass1 for biofuel

Up to now, the fast-growing switchgrass, because of its tough lignin, an organic polymer, has required heavy chemical treatment before it can be turned to ethanol as biofuel. Chuck’s gene transfer experiments have shown that because the improved switchgrass keeps the plants young, the lignin content of their cells is minimal and would need no… [Read More]

July 11, 2011

Mycosphaerella genome project in Capital Press

Septoria typically infects young seedlings that have recently emerged, creating lesions, and spreading to the higher leaves. It can affect yield and quality, Goodwin said. Control methods are typically fungicide sprays, he noted. Igor Grigoriev, of the U.S. Department of Energy’s Joint Genome Institute in Walnut Creek, Calif., has been sequencing the genomes of other… [Read More]

June 10, 2011

Mycosphaerella genome project in Agricultural Research

The pathogen that causes the disease, Mycosphaerella graminicola, has a long “silent period,” a latent stage during which it takes nutrition from the living plant and evades the host plant’s natural defenses. Scientists previously did not have a good understanding of how the organism infects wheat, or how the wheat plant itself resists the pathogen…. [Read More]

June 10, 2011

Mycosphaerella genome project in Farmers Guardian

SCIENTISTS have cracked the genetic code of septoria tritici – the most important foliar disease of wheat in the UK – and in doing so have gained an insight into how the disease is able to evade wheat’s natural defences. The researchers, who were funded by the BBSRC and others, hope the study, which reveals… [Read More]

June 10, 2011

First Finished Filamentous Fungus

An international consortium of scientists, including scientists from DOE JGI, have published the analysis for Mycosphaerella graminicola, the first filamentous fungus to be fully finished. Having the 39.7 million nucleotide genome available will enable researchers to learn more about the methods plant pathogens use to attack and damage crops, including those being considered for use… [Read More]

May 31, 2011

Poplar rust genome project on Wisconsin Ag Connection

The sequencing of the genetic codes of wheat stem rust pathogen (Puccinia graminis) and poplar leaf rust pathogen (Melampsora larici-populina) is expected to help researchers develop control strategies to address worldwide threats to wheat fields and tree plantations. The study, published in the Proceedings of the National Academy of Sciences, was a six-year collaborative effort… [Read More]

May 16, 2011

Maize genomics at DOE JGI User Meeting in Genome Technology

Speaking at the Department of Energy Joint Genome Institute’s sixth annual User Meeting, held in Walnut Creek, Calif., in March, Buckler said that while they may not have realized it at the time, maize breeders in Thailand, Mexico, and elsewhere have, since the turn of the 20th century, captured a great deal more genomic diversity… [Read More]

February 19, 2010

Brachy genome project on Federal Times

Federal researchers have been hard at work trying to develop alternate sources of clean renewable energy, and yesterday they announced a major breakthrough in their efforts. Scientists from the Agriculture Department and the Energy Department’s Joint Genome Institute for the first time have sequenced the genes of a wild grass species. The research, which is… [Read More]

February 18, 2010

Brachypodium genome project on Farm Futures

USDA scientists and their colleagues at the Department of Energy’s Joint Genome Institute say they have completed sequencing the genome of a kind of wild grass that will enable researchers to shed light on the genetics behind hardier varieties of wheat and improved varieties of biofuel crops. The grass, Brachypodium distachyon, can be used by… [Read More]

February 18, 2010

Brachypodium genome on ScienceDaily

Representative genomes for two of the three major subfamilies of grasses ⎯ those that include rice, maize, sorghum and sugar cane⎯ have already been sequenced. Now in the February 11 edition of the journal Nature, the International Brachypodium Initiative, a consortium which includes researchers from the DOE Joint Genome Institute (DOE JGI), presents the complete… [Read More]
Page 1 of 212»

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