The Department of Energy: Genome Sciences

1. 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 The Department of Energy:Genome Sciences

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

3. Provide the foundational science for: Developing biofuels as major, secure, and sustainable national energy resources Understanding potential effects of greenhouse gas emissions on Earth’s 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 BER Mission Drivers

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

5. 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) Office of Biological and Environmental Research

6. 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 The Microbe Project Interagency Working Group 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

7. “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.” The Microbe Project Interagency Working Group Goals for Research 1. Functional Genomics 2. Proteomics. 3. Comparative Genomics 4. Microbe-Host and Microbe-Microbe Interactions 5. Microbial Forensics 6. Environmental Genomics

8. http://www.jgi.doe.gov DOE Joint Genome Institute (JGI) “User facility providing high-throughput DNA sequencing & analysis in support of DOE missions in alternative energy, carbon cycling & bioremediation.”

9. 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 Community Sequencing Program

10. 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

11. ABI 3730 JJGI Sequencing Platforms Capillary[75] 1.8 Mb/day 700 bp reads $1000/Mb Plant WGS, Metagenomes, Clones 454/Roche[9] 600 Mb/day 400 bp reads $30/Mb Microbe WGS, Metagenomes, ESTs Solexa/Illumina[8] 1500 Mb/day 35 bp reads $10/Mb Re-sequencing, Transcript mapping

12. http://www.genomesonline.org/ Published Complete Genomes 1110 Archaeal complete genomes 111 Bacterial Ongoing Genomes:3342 Eukaryotic Ongoing Genomes 1165 Metagenomes 200 Total: 5928 Sequencing to Date (10/5/09)

13. Marsupials Birds Ruminants Mollusks Insects Compost Mammals Decomposing wood chips Bioenergy Metagenomes at the JGI

14. JGI GEBA

15. Plant Genomes Populus trichocarpa black cottonwood Chlamydomonas reinhardtii chlorophyte alga Physcomitrella patens bryophyte moss Sorghum bicolor sorghum Glycine max soybean Panicum virgatum switchgrass Miscanthus x giganteus miscanthus Volvox carteri multicellular 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 Setaria italica foxtail millet Capsella rubella Pink Shepherd’s purse Aquilegia coerulea Goldsmith columbine Gossypium raimondii diploid cotton Eucalyptus grandis rose gum Phaseolus vulgaris Common bean Zea mays (Mo17 inbred) maize

16. Single Cell Projects at the JGI DOEM 2007 Marine Flavobacteria sp. LSP 2007 Archaeal viral community R&D 2008 Green Sharpshooter Symbionts R&D 2009 Cow Rumen Community Ramunas Stepanauskas (Bigelow Lab) Howard Ochman (U of Arizona) Eddy Rubin (DOE JGI) Frank Roberto (Idaho Natl Lab) GEBA Tagetibacter soli Ellin 5290 GEBA Oscillospira guilliermondii GEBA Termite Gut Community 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 Maria Dominguez-Bello (UPR Rio Piedras) Daniel van der Lelie (Brookhaven Natl Lab) Gerald Tuskan (Oakridge Natl Lab) Daniel Distel (Ocean Genome Legacy) Tanja Woyke

18. Increasing Scale of Metagenomic Projects in the JGI’s Future Termite hindgut, 62 Mbp 62 Great Prairie metagenomic project , ~100 Gbp 100,000 1,000,000 Potential Future Projects: Terabase Projects 1 Terabase: 1 trillion (1012) base pairs

19. Eubacteria: 120 Plant (Eucalyptus) 1 Fungal: 37 Total: 158 JGI International Projects Integrated Microbial Genomes (IMG): http://img.jgi.doe.gov/cgi-bin/pub/main.cgi Integrated 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.

20. 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 Environmental Molecular Sciences Lab (EMSL) http://www.emsl.pnl.gov/emslweb/

21. 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

22. 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/

23. 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 4:30 p.m., Eastern Time, November 5, 2009. Closing Date for Applications: Jan 29, 2010 Program Manager: Susan K. Gregurick, susan.gregurick@science.doe.gov http://www.sc.doe.gov/grants/FOA-0000143.html

24. 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; Detlef Weigel, Max Planck Institute for Developmental Biology JGI Annual User Meeting: March 24-26, 2010, Walnut Creek, CA