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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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    (PXFuel)
    Designer DNA: JGI Helps Users Blaze New Biosynthetic Pathways
    In a special issue of the journal Synthetic Biology, JGI scientific users share how they’ve worked with the JGI DNA Synthesis Science Program and what they’ve discovered through their collaborations.

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    A genetic element that generates targeted mutations, called diversity-generating retroelements (DGRs), are found in viruses, as well as bacteria and archaea. Most DGRs found in viruses appear to be in their tail fibers. These tail fibers – signified in the cartoon by the blue virus’ downward pointing ‘arms’— allow the virus to attach to one cell type (red), but not the other (purple). DGRs mutate these ‘arms,’ giving the virus opportunities to switch to different prey, like the purple cell. (Courtesy of Blair Paul)
    A Natural Mechanism Can Turbocharge Viral Evolution
    A team has discovered that diversity generating retroelements (DGRs) are not only widespread, but also surprisingly active. In viruses, DGRs appear to generate diversity quickly, allowing these viruses to target new microbial prey.

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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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    This data image shows the monthly average sea surface temperature for May 2015. Between 2013 and 2016, a large mass of unusually warm ocean water--nicknamed the blob--dominated the North Pacific, indicated here by red, pink, and yellow colors signifying temperatures as much as three degrees Celsius (five degrees Fahrenheit) higher than average. Data are from the NASA Multi-scale Ultra-high Resolution Sea Surface Temperature (MUR SST) Analysis product. (Courtesy NASA Physical Oceanography Distributed Active Archive Center)
    When “The Blob” Made It Hotter Under the Water
    Researchers tracked the impact of a large-scale heatwave event in the ocean known as “The Blob” as part of an approved proposal through the Community Science Program.

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    A plantation of poplar trees. (David Gilbert)
    Genome Insider podcast: THE Bioenergy Tree
    The US Department of Energy’s favorite tree is poplar. In this episode, hear from ORNL scientists who have uncovered remarkable genetic secrets that bring us closer to making poplar an economical and sustainable source of energy and materials.

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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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    With a common set of "baseline metadata," JGI users can more easily access public data sets. (Steve Wilson)
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    Reflecting a structural shift in data access, the JGI Data Portal offers a way for users to more easily access public data sets through a common set of metadata.

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    Phytozome portal collage
    A More Intuitive Phytozome Interface
    Phytozome v13 now hosts upwards of 250 plant genomes and provides users with the genome browsers, gene pages, search, BLAST and BioMart data warehouse interfaces they have come to rely on, with a more intuitive interface.

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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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    Yeast strains engineered for the biochemical conversion of glucose to value-added products are limited in chemical output due to growth and viability constraints. Cell extracts provide an alternative format for chemical synthesis in the absence of cell growth by isolating the soluble components of lysed cells. By separating the production of enzymes (during growth) and the biochemical production process (in cell-free reactions), this framework enables biosynthesis of diverse chemical products at volumetric productivities greater than the source strains. (Blake Rasor)
    Boosting Small Molecule Production in Super “Soup”
    Researchers supported through the Emerging Technologies Opportunity Program describe a two-pronged approach that starts with engineered yeast cells but then moves out of the cell structure into a cell-free system.

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    These bright green spots are fluorescently labelled bacteria from soil collected from the surface of plant roots. For reference, the scale bar at bottom right is 10 micrometers long. (Rhona Stuart)
    A Powerful Technique to Study Microbes, Now Easier
    In JGI's Genome Insider podcast: LLNL biologist Jennifer Pett-Ridge collaborated with JGI scientists through the Emerging Technologies Opportunity Program to semi-automate experiments that measure microbial activity in soil.

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    A view of the mangroves from which the giant bacteria were sampled in Guadeloupe. (Hugo Bret)
    Giant Bacteria Found in Guadeloupe Mangroves Challenge Traditional Concepts
    Harnessing JGI and Berkeley Lab resources, researchers characterized a giant - 5,000 times bigger than most bacteria - filamentous bacterium discovered in the Caribbean mangroves.

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    In their approved proposal, Frederick Colwell of Oregon State University and colleagues are interested in the microbial communities that live on Alaska’s glacially dominated Copper River Delta. They’re looking at how the microbes in these high latitude wetlands, such as the Copper River Delta wetland pond shown here, cycle carbon. (Courtesy of Rick Colwell)
    Monitoring Inter-Organism Interactions Within Ecosystems
    Many of the proposals approved through JGI's annual Community Science Program call focus on harnessing genomics to developing sustainable resources for biofuels and bioproducts.

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    Coloring the water, the algae Phaeocystis blooms off the side of the sampling vessel, Polarstern, in the temperate region of the North Atlantic. (Katrin Schmidt)
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    As warm-adapted microbes edge polewards, they’d oust resident tiny algae. It's a trend that threatens to destabilize the delicate marine food web and change the oceans as we know them.

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Home › Our Projects › Legacy Projects › DOE Microbial Genome Program › FY2006 Sequencing for the DOE Microbial Genome Program

FY2006 Sequencing for the DOE Microbial Genome Program

For status information, see the Genome Projects section. For more information about the DOE Office of Science’s Microbial Genome Program, see http://microbialgenomics.energy.gov/.

Organism(s) Est. Genome Size
Anaeromyxobacter dehalogenans strain 2CP-1 5 MB
Acidithiobacillus ferrooxidans ATCC 53993
Anaeromyxobacter sp. Fw109-5 5 MB
Anaeromyxobacter sp. K 5 MB
Bison Pool, hydrothermal ecosystem NA
Burkholderia ambifaria MC40-6 7.4 MB
Burkholderia cenocepacia MC0-3 7.9 MB
Burkholderia multivorans ATCC 17616 6.8 MB
Burkholderia phymatum STM815 8.9 MB
Burkholderia phytofirmans PsJN 8 MB
Chlorella sp. NC64A 40 MB
Chlorella vulgaris C-169 40 MB
Clostridium cellulolyticum H10 5 MB
Comamonas testosteroni KF-1 6 MB
Dehalococcoides sp. Strain GT 1.5 MB
Delftia acidovorans SPH-1 6 MB
Desulfatibacillum alkenivorans AK-01 6 MB
Desulfococcus oleovorans Hxd3 6 MB
Dictyostelium purpureum 34 MB
Dinoroseobacter shibae DFL-12 6 MB
Dunaliella salina UTEX 130 MB
Enterobacter sp. 638 , 5 MB
Escherichia coli C str. ATCC 8739 4 MB
Geobacter Lovleyi SZ 4 MB
Leptospirillum ferroxidans Markosian 2.5 MB
Marinomonas sp. strain MWYL1 5 MB
Metallosphaera sedula DSM 5348 1.89 MB
Methanococcus aeolicus Nankai-3 2 MB
Methanococcus maripaludis C5 2 MB
Methanococcus maripaludis C6 2 MB
Methanococcus maripaludis C7 2 MB
Methanococcus vannielii SB 2 MB
Methanococcus voltae A3 2 MB
Methanoregula boonei 6A8 3 MB
Methylobacterium chloromethanicum CM4 7 MB
Methylobacterium extorquens PA1 7 MB
Methylobacterium nodulans ORS 2060 7 MB
Methylobacterium populi BJ001 7 MB
Methylobacterium radiotolerans JCM 2831 7 MB
Methylobacterium sp. 4-46 7 MB
Methylotroph strain L1N13 10 MB
Nitrosopumilus maritimus SCM1 3 MB
Parvibaculum lavamentivorans DS-1 6 MB
Plasmids in prokaryotes 7 MB
Poplar endophytic bacteria (Pseudomonas putida strain W619, Serratia proteamaculans 568, Stenotrophomonas maltophilia R551-3) 37.3 MB
Prochlorococcus, its phages, and the surrounding microbial community at the Hawaii Ocean Times Series Station (HOT) 2 GB
Pseudomonas mendocina strain ymp 4.6 MB
Pseudomonas putida strain GB-1 6 MB
Pseudo-nitzschia (diatom) 250 MB
Ralstonia pickettii 12D 3 MB
Ralstonia pickettii 12J 3.5 MB
Rice endophyte metagenome 100 MB
Schizophyllum commune 38 MB
Shewanella halifaxensis HAW-EB4 5 MB
Shewanella pealeana ATCC 700345 5 MB
Shewanella sediminis HAW-EB3 5 MB
Shewanella woodyi ATCC 51908 5 MB
Sphingomonas wittichii Strain RW1 5 MB
Sulfolobus islandicus strains (eight) 24 MB
Thermosinus carboxydivorans Nor1 3 MB
Trichoderma actroviride 40 MB

 

  • Laboratory Science Program Small-Scale Sequencing Plans
  • DOE Microbial Genome Program
    • FY2007 Sequencing for the DOE Microbial Genome Program
    • FY2006 Sequencing for the DOE Microbial Genome Program
    • FY2005 Sequencing for the DOE Microbial Genome Program
    • FY2004 Sequencing for the DOE Microbial Genome Program
    • FY2003 Sequencing for the DOE Microbial Genome Program
    • FY2002 Sequencing for the DOE Microbial Genome Program
    • FY2001 Sequencing for the DOE Microbial Genome Program
  • Sequencing for the DOE Genomics: GTL Program
  • DOE Sequencing Projects

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