The Department of Energy: Genome Sciences

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The Department of EnergyGenome Sciences
NRC Designing the Microbial Commons

• Daniel Drell, Ph.D.
• Biological Systems Science Division
• Office of Biological and Environmental Research
• U.S. Department of Energy
• October 9, 2009

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Steven Chu, Secretary, Department of Energy
Steve Koonin, Undersecretarry for Science
William Brinkman, Director, Office of Science
Advanced Scientific Computing Research
Fusion Energy Sciences
High Energy Physics
Basic Energy Sciences
Nuclear Physics
Biological and Environmental Research (BER) Anna
PalmisanoAssociate Director
Climate and Environmental Sciences Michael
Kuperberg Acting Director
Biological Systems Science Sharlene
Weatherwax Director
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BER Mission Drivers

• Provide the foundational science for
• Developing biofuels as major, secure, and
  sustainable national energy resources
• Understanding potential effects of greenhouse gas
  emissions on Earths climate and biosphere and
  the implications of these emissions for our
  energy future
• Predicting the fate and transport of contaminants
  in the subsurface environment at DOE sites
• Developing new tools to explore the interface of
  biological and physical sciences

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Major DOE Missions

• Biological generation of energy compounds
  (biofuels) e.g. Hydrogen, Ethanol
• Biogeochemistry of legacy wastes (metals,
  radionuclides, toxic chemicals, etc.)
• Carbon Dioxide Capture and Sequestration

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Office of Biological and Environmental Research

• Biological Systems Science Division
• Genome Sciences
• (Knowledgebase)
• Bioenergy Research Centers
• Imaging
• Radiobiology
• Ethical, Legal, and Social Issues (ELSI)
• User Facilities (JGI)
• Climate and Environmental Sciences Division
• Atmospheric Systems Research
• Environmental Systems Science
• Climate and Earth Systems Modelnig
• User Facilities (ARM, EMSL)

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The Microbe Project Interagency Working Group

• Daniel Drell (Chair) DOE Frederick Pearce DOD
• Ann Lichens-Park (Exec Sec) USDA Robert Foster
  DOD
• Joanne Tornow NSF James Lindsay USDA
• Maria Giovanni NIH Kevin Anderson DHS
• James Anderson NIH C. Jacobs-Young OSTP
• Kay Marano Briggs DOI Gerard Stelma EPA
• Michael Broder EPA
• Linda Chrisey ONR
• Valentina Di Francesco NIH
• J. Eugene LeClerc FDA
• Pamela McInnes NIH
• Shawn McLaughlin NOAA
• Dale Nordenberg CDC

Member agencies DOE, CSREES/USDA, NSF, ARS/USDA,
NIAID/NIH, NIDCR/NIH, NIGMS/NIH, EPA, FDA,
USGS/DOI, ONR/DOD, NOAA, CDC, DST/DOD, DHS, OSTP
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The Microbe Project Interagency Working Group

• Maximize the opportunities offered by
  genome-enabled microbial science to benefit
  science and society through coordinated
  interagency efforts to promote research,
  infrastructure development, education and
  outreach.

Goals for Research 1. Functional Genomics 2.
Proteomics. 3. Comparative Genomics 4.
Microbe-Host and Microbe-Microbe Interactions 5.
Microbial Forensics 6. Environmental Genomics
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DOE Joint Genome Institute (JGI)
http//www.jgi.doe.gov
User facility providing high-throughput DNA
sequencing analysis in support of DOE missions
in alternative energy, carbon cycling
bioremediation.
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Community Sequencing Program

• Targets sequence-based projects of high
  scientific merit
• Focus on DOE relevance
• JGI organizes peer-review, allocation 50 of
  capacity
• Approved for sequencing (2005-2009)
• 174 bacterial archaeal isolates
• 33 metagenomes
• 45 fungi, algae
• 20 euk pilots EST projects
• 17 plant animal WGS
• http//www.jgi.doe.gov/CSP/
• http//img.jgi.doe.gov/cgi-bin/pub/main.cgi

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JGI Science Programs
Prokaryotic Isolates Tanja Woyke Nikos
Kypides Jonathan Eisen
Fungi Scott Baker Alla Lapidus Igor Gregoriev
Plants Dan Rokhsar Jeremy Schmutz Jerry Tuskan
Metagenomes Phil Hugenholtz Susannah Tringe Nikos
Kyrpides
IMG, IMG/M
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Sequencing Platforms
JJGI
Capillary75 1.8 Mb/day 700 bp reads
1000/Mb Plant WGS, Metagenomes, Clones
454/Roche9 600 Mb/day 400 bp reads 30/Mb Microb
e WGS, Metagenomes, ESTs
Solexa/Illumina8 1500 Mb/day 35 bp
reads 10/Mb Re-sequencing, Transcript mapping
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Sequencing to Date (10/5/09)

• http//www.genomesonline.org/
• Published Complete Genomes 1110
• Archaeal complete genomes 111
• Bacterial Ongoing Genomes 3342
• Eukaryotic Ongoing Genomes 1165
• Metagenomes 200
• Total 5928

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Bioenergy Metagenomes at the JGI
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JGI GEBA
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Plant Genomes
Populus trichocarpa black cottonwood Chlamydomo
nas reinhardtii chlorophyte alga
Physcomitrella patens bryophyte moss Sorghum
bicolor sorghum Glycine max soybean Panicum
virgatum switchgrass Miscanthus x
giganteus miscanthus Volvox carteri multicell
ular green alga Arabidopsis lyrata Lyrate
rockcress Selaginella moellendorffii lycophyte
fern Brachypodium distachyon false purple
brome Mimulus guttatus monkeyflower Manihot
esculenta c assava Prunus persica peach Setar
ia italica foxtail millet Capsella
rubella Pink Shepherds purse Aquilegia
coerulea Goldsmith columbine Gossypium
raimondii diploid cotton Eucalyptus
grandis rose gum Phaseolus vulgaris Common
bean Zea mays (Mo17 inbred) maize
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Single Cell Projects at the JGI
LSP 2007 Archaeal viral community
RD 2008 Green Sharpshooter Symbionts
RD 2009 Cow Rumen Community
DOEM 2007 Marine Flavobacteria sp.
Frank Roberto (Idaho Natl Lab)
Howard Ochman (U of Arizona)
Eddy Rubin (DOE JGI)
Ramunas Stepanauskas (Bigelow Lab)
GEBA Oscillospira guilliermondii
GEBA Termite Gut Community
GEBA Tagetibacter soli Ellin 5290
Single Cell Projects at the JGI
Catherine Osborne (UC Berkeley)
Roderick Mackie (U of Illinois)
Phil Hugenholtz (DOE JGI)
DOEM 2004 Glomus intraradices
CSP 2009 Shipworm symbionts
CSP 2009 Hoatzin crop microbiome
BESC 2008 Clostridium pasteurianum BC1
Gerald Tuskan (Oakridge Natl Lab)
Daniel Distel (Ocean Genome Legacy)
Maria Dominguez-Bello (UPR Rio Piedras)
Daniel van der Lelie (Brookhaven Natl Lab)
Tanja Woyke
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Increasing Scale of Metagenomic Projects in the
JGIs Future
1 Terabase 1 trillion (1012) base pairs
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JGI International Projects

• Eubacteria 120
• Plant (Eucalyptus) 1
• Fungal 37
• Total 158

Integrated Microbial Genomes (IMG)
http//img.jgi.doe.gov/cgi-bin/pub/main.cgi Integr
ated Microbial Genomes Microbiome Samples
http//img.jgi.doe.gov/cgi-bin/m/main.cgi IMG is
a data management and analysis platform,
containing draft and completed genomes, from the
JGI and elsewhere in the public domain, providing
tools and viewers for analyzing genes and
genomes, singly or comparatively, and generate
GenBank formatted files.
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Environmental Molecular Sciences Lab (EMSL)

• EMSL Capabilities
• Nuclear Magnetic Resonance EPR
• Mass Spectrometry
• Kinetics Reactions
• Molecular Science Computing
• Subsurface Flow and Transport
• Deposition and Microfabrication
• Spectroscopy Diffraction
• Science Themes
• Biological Interactions and Dynamics
• Biogeochemistry and Subsurface Science
• Interfacial Processes

http//www.emsl.pnl.gov/emslweb/
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GTL Data and Information Sharing Policy

• The Office of Biological and Environmental
  Research (OBER) will require that all publishable
  information resulting from GTL funded research
  must conform to community recognized standard
  formats when they exist, be clearly attributable,
  and be deposited within a community recognized
  public database(s) appropriate for the research
  conducted. Furthermore, all experimental data
  obtained as a result of GTL funded research must
  be kept in an archive maintained by the Principal
  Investigator (PI) for the duration of the funded
  project. Any publications resulting from the use
  of shared experimental data must accurately
  acknowledge the original source or provider of
  the attributable data.

• JGI Data Release Policy (http//genome.jgi-psf.org
  /pages/data-usage-policy.jsf)
• Immediate release of raw reads
• reserved analyses are discouraged (for up to
  but not more than 12 months) when they would
  compete with scientific aims of the project PI

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A Knowledgebase Workshop to define Needs and
provide Recommendations Held May 28-30, 2008 in
Washington DC and Chaired by Jim Frederickson
and Rick Stevens

• To accelerate research on the integration, cross
  referencing, genertion and ongoing curation of
  derived data to make the genomic/biological
  communities more effective.
• To provide a variety of interfaces, suitable for
  both first time and more experienced users and
  to provide useful applications and interfaces.
• To leverage best-in-class existing tools,
  standards, protocols and database technologies
  and to stimulate development of new and improved
  tools.

http//genomicsgtl.energy.gov/compbio/
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Office of Science Financial Assistance Funding
Opportunity Announcement DE-FOA-0000143
Computational Biology and Bioinformatic Methods
to Enable a Systems Biology Knowledgebase

• There are four objectives that may be addressed
  by applicants responding to this FOA
• develop methods to integrate together multiple
  data types,
• develop new methods to infer and curate
  (meta)genomic functional annotations
• develop methods to couple multiple cellular
  pathways and processes and
• develop new methods to model whole cellular
  processes.

Preapplication due to DOE by 430 p.m., Eastern
Time, November 5, 2009. Closing Date for
Applications Jan 29, 2010    Program Manager
Susan K. Gregurick, susan.gregurick_at_science.doe.g
ov http//www.sc.doe.gov/grants/FOA-0000143.html

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JGI Annual User Meeting March 24-26, 2010,
Walnut Creek, CA

• Genomics of Energy Environment
• Genomics of renewable energy strategies, carbon
  cycling, environmental gene discovery, and
  engineering of fuel-producing organisms
• Http//www.jgi.doe.gov/meetings/usermeeting
• Rita Colwell, Chairman of Canon US Life Sciences
  U Maryland
• Cristina Cuomo, Broad Institute
• Evan Delucia, University of Illinois at
  Urbana-Champaign
• Richard Flavell, Ceres Dennis Hedgecock,
  University of Southern California
• Jay Keasling, CEO DOE Joint BioEnergy Institute
• Richard Jorgensen, iPlant Collaborative,
  University of Arizona
• Madhu Khanna, University of Illinois at
  Urbana-Champaign
• Steve Knapp, University of Georgia
• Tom Mitchell-Olds, Duke University
• Steve Moose, University of Illinois at
  Urbana-Champaign
• Joseph Noel, Salk Institute for Biological
  Studies
• Forest Rohwer, San Diego State University
• Steven Savage, Cirrus Partners
• Gary Stacey, University of Missouri
• Jim Tiedje, Michigan State University