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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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    Abstract image of gold lights and squares against a black backdrop
    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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News & Publications
Home › News Releases
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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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