1. Advancing Science with DNA Sequence Response to BERAC Review Overview of JGI BERAC Recommendations –Managing multi-lab environment –Operation of user facility –LSP program JGI Energy Portfolio

2. Advancing Science with DNA Sequence JGI Mission “User facility providing DNA sequencing & analysis in support of DOE missions in alternative energy, carbon cycling & bioremediation.” www.jgi.doe.gov

3. Advancing Science with DNA Sequence Cost-effective Sequencing at JGI NIH data provided by Jane Peterson, NHGRI Cntr1Cntr4Cntr3Cntr2Cntr5Cntr6JGI FY06 capacity: 30 billion basepairs

4. Advancing Science with DNA Sequence Success of JGI User Programs Microbial Genome ProgramProposed Accepted Community Sequencing ProgramProposed Accepted

5. Advancing Science with DNA Sequence Primary JGI User Distribution KEY: RED=Academic; Blue=National Laboratory; Black=Industry

6. Advancing Science with DNA Sequence 1 st Annual JGI User Meeting JGI User Meeting, April 2006 250 Users and potential users Sequence-based science talks Tours of JGI facility Poster sessions User Committee formed

7. Advancing Science with DNA Sequence JGI Director PGF LBNL LANL ORNL LLNL SHGCPNNL The JGI Partnership Managing in a multi-lab environment: Dual workforce at PGF Succession planning at PGF Coordination of partner tasks

8. Advancing Science with DNA Sequence BERAC Recommendations Operations and Management-1 Management of LBL/LLNL workforce –Coordination of safety training & tracking EH&S MOU complete, waiting signatures LBL has 1º responsibility for EH&S –Cyber-security MOU Committee configured, meets this month

9. Advancing Science with DNA Sequence BERAC Recommendations Operations and Management-2 Succession planning for key JGI positions –Hired production sequencing lead –Senior managers identified “seconds” –Seconds contribute to weekly mgmt meetings

10. Advancing Science with DNA Sequence BERAC Recommendations Operations and Management-3 Coordination of JGI partner lab tasks: Weekly genome management conference call Monthly partners conference call “Finishing in the future” meeting Eukaryotic Genome Program summit

11. Advancing Science with DNA Sequence BERAC Recommendations User Facility Proposals Sequencing Annotation User Agreement DNA Libraries Asssembly Sequencing scales easily Efficiency of the user facility: Peer review Project management Assembly & annotation throughput

12. Advancing Science with DNA Sequence BEERAC Recommendations User Facility-1 Managing the User Facility: –Peer review MGP and CSP programs/review groups merged Broadened geographical representation Electronic proposal submission & review Letter-of-intent process User committee input on peer review committees

13. Advancing Science with DNA Sequence BEERAC Recommendations User Facility-2 Managing the User Facility: –Formal project management Appointed project management lead Hired 2 new project managers Launched Global Project Tracking System End-of-project survey in draft form

14. Advancing Science with DNA Sequence BERAC Recommendations User Facility-3 Managing the User Facility: –Improve large genome analysis throughput JAZZ assembly program overhauled 2 programmers hired into assembly group 3 people hired into annotation group

15. Advancing Science with DNA Sequence Lab Science Program LSP created by new JGI MOU –Facilitate access to JGI for Natl. Lab investigators –Fulfill programmatic sequencing needs of DOE –Shape JGI products and services to meet needs of the Natl. Labs BERAC concerns –Scientific vision for LSP –Implementation

16. Advancing Science with DNA Sequence BERAC Recommendations LSP Program LSP lead –Appointed Jerry Tuskan, ORNL, Jan ‘06 –Focus on bioenergy –LSP lead now reports to JGI Director Implementation –Lab points-of-contact identified –Small-scale sequencing program 14 proposals received, 10 approved to date –Large-scale sequencing program Plant Genomes for Energy white paper Fungal Genomes for Energy white paper

17. Advancing Science with DNA Sequence Petroleum – 98% 2% Bioenergy & the JGI Corn based ethanol Soy-based biodiesel NSF/USDA/DOE funded project LSP project Transportation Fuels

18. Advancing Science with DNA Sequence JGI and Bioenergy Fermentation Saccharification Sugars Improved Feedstocks Improved cellulose & lignin degradation Ethanol producing organisms Cellulose Termite hindgut microbiota White Rot Fungus Clostridium thermocellum Saccharophagus degradans Acidothermus cellulolyticus Saccharomyces cerevisiae Zymomonas mobilis Thermoanaerobacter ethanolicus Pichia stipitis Cellulosic Materials Poplar Maize/Corn Stover Switchgrass Brachypodium Sorghum

19. Advancing Science with DNA Sequence Auxin Regulation of Poplar Shape Enhanced radial growth of IAA16.3 transgenic trees IAA16.3 Control 90-day-old Populus cuttings stem cross sectional area (cm) transgenic control 7.1 4.4

20. Advancing Science with DNA Sequence Glc H2OH2O 22  -glucosidase P GlcGlc-1-P P Cellobiose phosphorylase 12 Exoglucanases Cellulose Cellobiose 15 Endoglucanases New Cellulase Genes from Termite Gut