U.S. JOINT DEPARTMENT GENOME OF ENERGY INSTITUTE PROGRESS REPORT 2007 On the cover: The eucalyptus tree was selected in 2007 for se- quencing by the JGI. The microbial community in the termite hindgut of Nasutitermes corniger was the subject of a study published in the November 22, 2007 edition of the journal, Nature. JGI Mission The U.S. Department of Energy Joint Genome Institute, supported by the DOE Office of Science, unites the expertise of five national laboratories—Lawrence Berkeley, Lawrence Livermore, Los Alamos, Oak Ridge, and Pacific Northwest — along with the Stanford Human Genome Center to advance genomics in support of the DOE mis- sions related to clean energy generation and environmental char- acterization and cleanup. JGI’s Walnut Creek, CA, Production Genomics Facility provides integrated high-throughput sequencing and computational analysis that enable systems-based scientific approaches to these challenges. U.S. DEPARTMENT OF ENERGY JOINT GENOME INSTITUTE PROGRESS REPORT 2007 JGI PROGRESS REPORT 2007 Director’s Perspective . 4 JGI History. 7 Partner Laboratories . 9 JGI Departments and Programs . 13 JGI User Community . 19 Genomics Approaches to Advancing Next Generation Biofuels . 21 JGI’s Plant Biomass Portfolio . 24 JGI’s Microbial Portfolio . 30 Symbiotic Organisms . 30 Microbes That Break Down Biomass . 32 Microbes That Ferment Sugars Into Ethanol . 34 Carbon Cycling . 39 Understanding Algae’s Role in Photosynthesis and Carbon Capture . 39 Microbial Bioremediation . 43 Microbial Managers of the Nitrogen Cycle . 43 Microbial Management of Wastewater . 44 Exploratory Sequence-Based Science . 47 Genomic Encyclopedia for Bacteria and Archaea (GEBA) . 47 Functional Analysis of Horizontal Gene Transfer . 47 Anemone Genome Gives Glimpse of Multicelled Ancestors . 48 DNA Sequence Analysis Tools . 50 Integrated Microbial Genomes (IMG) Data Management System . 50 IMG/M “Gold Standard” for Metagenome Analysis . 51 New Sequencing Technologies . 52 Education and Outreach . 57 Safety and Ergonomics . 59 Awards and Honors . 61 Appendices Appendix A: JGI Sequencing Process . 62 Appendix B: Genomics Glossary. 64 Appendix C: Community Sequencing Program . 66 Appendix D: Laboratory Science Program . 70 Appendix E: Review Committees and Board Members . 71 Appendix F: 2007 JGI User Meeting Agenda Speakers List . 74 Appendix G: 2006-2007 Publications . 75 DIRECTOR’S PERSPECTIVE In this past year, we have seen a continuing emphasis on the impor- tance of developing biologically- derived alternatives to fossil fuels driven by a confluence of political, economic, and environmental fac- tors. In connection with this, the De- partment of Energy recently funded three new Bioenergy Research Centers to accelerate basic research for the development of cellulose- derived fuels. The JGI will play an important role—through sequenc- ing selected genomes and con- ducting data analysis—in enabling the groundbreaking science of these Centers. While the JGI will sustain its other user programs, the DOE Bioenergy Research Centers rep- resent a substantial and important metric of nucleotides sequenced, ipants to Walnut Creek, California. new community of users for the JGI. but a more important measure is the This event provided a forum for in- increasing number of researchers vestigators to discuss sequence- The Community Sequencing Pro- whose science was enabled by the based science, genomic applications gram (CSP), now in its fourth year, new data and its analysis available to issues of bioenergy, carbon cy- continues to be the main conduit from the various JGI databases. cling, and bioremediation, and in- for our users. The largest CSP proj- This contribution is only in part re- formatics tools for sequence ect that the JGI will be tackling in flected in the peer-reviewed publi- analysis. In addition to the user the next year is the eucalyptus tree cations authored by JGI researchers. meeting, the JGI hosted numerous genome. As is typical for many JGI During 2006–2007, JGI and its col- informatics workshops, annotation projects, the consortium of inves- laborators published over 170 pa- jamborees, and focused meetings tigators who proposed this effort pers, with more than 20 papers in the throughout the year at the JGI’s draws expertise from dozens of in- journals Science and Nature. These Walnut Creek Production Ge- stitutions and hundreds of re- papers have ranged from an analy- nomics Facility (PGF). searchers worldwide. Eucalyptus sis of microbial communities in the are rapidly growing trees, and likely termite hindgut as a means to iden- A crucial change presently under- to gain more attention as a prospec- tify cellulose-degrading machinery, way at the PGF is a technological tive bioenergy crop. Knowledge of to revealing the genes of a green one. For the past 20-plus years, the this genome will accelerate the alga genome and how its genes Sanger-based sequencing process work of researchers who are seeking enable efficient carbon capture. dominated how sequencing was to adapt this tree and other plant done. Over the years, as this tech- species as a biomass feedstock. The JGI hosts a variety of forums nology has yielded increases in to encourage interactions with its throughput and reduction in costs, The JGI’s productivity in the past users. In March, the JGI’s annual the number of JGI’s Sanger-based year can be assessed in the basic user meeting drew over 400 partic- sequencing machines eventually 4 grew to more than 110. Recently, a new generation of sequencers has emerged, offering even more spec- tacular economies of scale and ca- pability. Accordingly, the JGI has Essential to the efficient operation years on our Walnut Creek facility— been exploring how to add these of the JGI is maintaining a safe our home for the entirety of the new platforms and their capabili- workplace and a motivated work- JGI’s 10-year history. It is only with ties to meet JGI’s sequencing force. Understanding that the na- support from the Department of needs. This last summer, as part of ture of production sequencing is Energy and the University of Cali- that transition, the JGI retired 36 repetitive, the JGI has taken enor- fornia that we were able to marshal Sanger-based DNA sequencers mous care to monitor various as- the resources to secure our future. and has added several next-gener- pects of the production activities This new lease will enable us to ex- ation sequencers to the DNA se- and to implement the necessary pand our campus, to consolidate quencing production line. changes to ensure a safe work- our administrative and informatics place. Despite our efforts and suc- staff, and effectively meet the ex- With these new technologies, DNA cesses, ergonomics remains a panding thirst for DNA sequence sequencing centers, such as the serious concern at the PGF. For the and analysis. JGI, have progressively become month of December, 2007, rein- fire hoses of DNA sequence data forcing our commitment to main- We look ahead to contributing to with the accompanying challenge tain a safe workplace, we seized an advances that will be catalyzed at of supplying this information to opportunity to step back from the the interface of biology, information users in an accessible form. In re- day-to-day production schedule to technology, energy, and the envi- sponse to this challenge, the JGI is evaluate our standard operating ronment. I encourage you to read engaged in developing new ways procedures and implement bot- on about the successes of the JGI to improve community access to tom-to-top process improvements. in the past year—and our prospects its data. This has included increases for the future. in our informatics capabilities, im- On the operations front, a crucial provements in our plant and mi- accomplishment in the past year Edward M. Rubin, MD, PhD crobial portals, as well as expansion has been securing a five-year lease Director of our educational activities. with an option for an additional five DOE Joint Genome Institute 5 6 JGI HISTORY The U.S. Department of Energy Joint Genome Institute (JGI) was created in 1997 to unite the expertise and resources in genome mapping, DNA se- quencing, technology development, and information sciences pioneered at the DOE genome centers at Lawrence Berkeley National Laboratory (LBNL), Lawrence Livermore National Laboratory (LLNL), and Los Alamos National Laboratory (LANL). In 1999, the University of California, which managed the three national labs for the DOE, leased 60,000 square feet of laboratory and office space in a light industrial park in Walnut Creek, California, to consolidate activities and accommodate the JGI’s growing workforce in what is now known as the Production Genomics Facility (PGF). In 2004, with the successful completion of the human genome, the JGI re- oriented its focus to become a user facility driven by DOE mission needs in the areas of bioenergy, carbon cycling, and bioremediation. This transition has benefited from broader involvement of the DOE national laboratory sys- tem, including the formal participation of Oak Ridge National Laboratory (ORNL), Pacific Northwest National Laboratory (PNNL), and the Stanford Human Genome Center, in the activities of the JGI. The importance of the JGI as essential infrastructure for DOE science was codified through sign- ing of a new MOU between the five partner labs in 2006. In 2007, with the launching of the three DOE Bioenergy Research Centers (http://genomicsgtl.energy.gov/centers/) to accelerate basic research in the development of next-generation biofuels, the JGI was acknowledged as a vital contributor in its capacity to provide DNA sequencing and its analysis in support of these centers. For more information about the JGI’s history, facility, partners, and science, visit our Web site at http://www.jgi.doe.gov/whoweare/index.html. 7 8 PARTNER LABORATORIES The JGI primarily draws its employees for the Production Genomics Facility employee Patrick Chain led this im- (PGF) in Walnut Creek, California, from Lawrence Berkeley National Laboratory portant activity.