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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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Our Projects
Home › Our Projects › Legacy Projects › Laboratory Science Program Small-Scale Sequencing Plans

Laboratory Science Program Small-Scale Sequencing Plans

For status information, see the Genome Projects section.

Organism Proposer Affiliation
Five Archaea (Methanohalobium evestigatum, Methanobacterium formicicum, Halococcoides, Ferroglobus placidus, and Acidianus sp. JP7) Kyrpides LBNL
Aspergillus terreus EST Baker PNNL
Avena Barbata ESTs Anderson BNL
Burkholderia cepacia Bu72 van der Lelie BNL
ChIP-enriched binding sequences Stubbs LLNL
CRISPR loci of Leptospirillum Banfield
Cochliobolus heterostrophus Turgeon Cornell University
Columbia River Microbiota Magnuson PNNL
Dehalococcoides Brodie LBNL
Etolico Lagoon in Greece Kyrpides LBNL
Fungal comparative genomics (Orpinomyces) Baker PNNL
Hypersaline microbial mat Raymond LLNL
Leonotis nepetifolia Shanklin BNL
Low Dose DiTags Anderson BNL
Medaka Fish Glenn SRNL
Microbial community actively decaying poplar biomass van der Lelie BNL
Microbial diversity in tropical and temperate forests Pett-Ridge LLNL
Microcoleus vaginatus FGP-2 Kuske LANL
New Orleans Floodwaters Andersen LBNL
Nuclear matrix attachment regions (MARs) Doggett LANL
Peromyscus Glenn SRNL
Phycomyces blakesleeanus Baker PNNL
Poplar in Response to Dehydration Yang ORNL
Prunus persica Rokhsar LBNL
Soluble protein domains Terwilliger LANL
Tallgrass Prairie soil Bailey PNNL
Grass-feeding termite hindgut communities Hugenholtz LBNL
Thielavia terrestris Berka Novozymes
Tremella mesenterica Heitman Duke University
Viruses in nasopharyngeal swab samples from healthy subjects Mariella LLNL
454 Sequencing of Viruses Han LANL
Yellowstone Archaeal Virus Community (Nymph Lake and Crater Hills) Roberto INL
  • Laboratory Science Program Small-Scale Sequencing Plans
  • DOE Microbial Genome Program
  • Sequencing for the DOE Genomics: GTL Program
  • DOE Sequencing Projects

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