Joint Meeting - Genomics - U.S. Department of Energy

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The following table is a simple summation of how GTL science and DOE missions align (GTL Roadmap p. 40). Summary Table. GTL Science Roadmap for DOE Missions A capsule summary of systems being studied, mission goals that drive the analysis, generalized science roadmaps, and outputs to DOE missions. To elucidate design principles, each of these goals entails the examination of thousands of natural primary and ancillary pathways, variants, and functions, as well as large numbers of experimental mutations.
Milestone 1 Section 1 Organism Sequencing, Annotation, and Comparative Genomics 1 U.S. DOE Joint Genome Institute Microbial Sequencing: Genomes to Life Projects The Code—Understand Gene Structure and Functional Potential of Plants and Microbes and Their Communities David Bruce 1 * (dbruce@lanl.gov), Tom Brettin 1 , Patrick Chain 3 , Cliff Han 1 , Loren Hauser 5 , Nikos Kyrpides 2 , Miriam Land 5 , Alla Lapidus 2 , Frank Larimer 5 , Jeremy Schmutz 4 , Paul Gilna 1 , Eddy Rubin 2 , and Paul Richardson 2 1 JGI-Los Alamos National Laboratory, Los Alamos, NM; 2 JGI-Production Genomics Facility and Lawrence Berkeley National Laboratory, Berkeley, CA; 3 JGI-Lawrence Livermore National Laboratory, Livermore, CA; 4 JGI-Stanford Human Genome Center, Palo Alto, CA; and 5 JGI-Oak Ridge National Laboratory, Oak Ridge, TN The US DOE Joint Genome Institute (JGI) sequences microbial and metagenomic projects through three main programs: DOE Microbial Genome Program (MGP), JGI Community Sequencing Program (CSP) and DOE Genomes to Life Program (GTL). The principle goal of the MGP is to fund sequencing projects related to DOE interests, the principle goal of the CSP is to fund sequencing projects from a broad range of disciplines that may not be covered in the MGP, and the principle goal of the GTL sequencing projects is to fund sequencing projects in direct support of the GTL program. The JGI is responsible for sequencing, assembling, annotating microbial genomes, and publishing sequence and annotation in GenBank and the DOE JGI Integrated Microbial Genomics web based system. The JGI has sequenced nearly 250 microbes and metagenomic samples to draft quality and completely finished over 120 microbes. Most microbial projects are targeted for finishing. The overall capacity is now approximately 100-125 microbial projects per year through draft sequencing and finishing. Virtually all microbial projects are sequenced by the whole genome shotgun method. To being the sequencing process, the Library group randomly shears the purified DNA under different conditions and selects for three size populations. Fragments are end repaired and selected for inserts in the range of 3kb, 8kb, and 40kb. These are cloned into different vector systems and checked for quality by PCR or sequencing. The libraries are sequenced by the Production group to approximately 8.5X coverage. The resulting reads are trimmed for vector sequences and assembled. The assembly is quality checked, automatically annotated by the Annotation group, and released to the collaborating PI as the initial Quality Draft assembly. For finishing, the draft assembly is assigned to a Finishing group. The Finishing group closes all sequence gaps, resolves all repeat discrepancies, and improves all low quality regions. The final assembly is then passed to the Quality Assurance group to assess the integrity and overall quality of the genome sequence. The finished sequence then receives a final annotation and this package is used as the basis for analysis and publication in GenBank and the DOE JGI Integrated Microbial Genomics web based system. The JGI is made up of affiliates from a number of national laboratories including Lawrence Berkeley National Laboratory, Lawrence Livermore National Laboratory, Los Alamos National Laboratory, Oak Ridge National Laboratory, and the Stanford Human Genome Center. * Presenting author 3
Page 1: Joint Meeting Genomics:GTL Contract
Page 5 and 6: * Presenting author Contents Welcom
Page 7 and 8: Poster Page 16 Environmental Whole-
Page 9 and 10: Poster Page 35 Complementary Assays
Page 11 and 12: Poster Page 50 The MAGGIE Project:
Page 13 and 14: Poster Page 64 Comparative Analysis
Page 15 and 16: Poster Page 81 Comprehensive Study
Page 17 and 18: Poster Page 102 Reverse-Engineering
Page 19 and 20: Poster Milestone 3 Computing Infras
Page 21: This is the first Genomics:GTL work
Page 25 and 26: Organism Sequencing, Annotation, an
Page 27 and 28: 6. 7. 8. 9. 10. 11. Organism Sequen
Page 41 and 42: Section 2 Microbial-Community Seque
Page 43 and 44: Microbial-Community Sequencing 15 C
Page 45 and 46: Microbial-Community Sequencing nati
Page 47 and 48: 19 Understanding Phage-Host Interac
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Page 51 and 52: Protein Production and Characteriza
Page 54 and 55: Milestone 1 25 Development of Genom
Page 56 and 57: Milestone 1 27 High-Throughput Meth
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Page 62 and 63: Milestone 1 33 Comparison of Conser
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Milestone 1 41 Protein Complex Anal
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Milestone 1 to the absence of compo
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Milestone 1 44 A Hybrid Cryo-TEM an
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Milestone 1 45 Optical Methods for
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Milestone 1 of these proteins are k
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Milestone 1 48 Cell-Permeable Multi
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Milestone 1 50 The MAGGIE Project:
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Milestone 2 Section 1 OMICS: System
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OMICS: Systems Measurements of Plan
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Stress Experiments OMICS: Systems M
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Figure 3. (A) Abrupt changes in flu
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conditions, suggesting a regulatory
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Milestone 2 addition, we designed a
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Milestone 2 72 The Use of Microbial
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Milestone 2 Validation of c-Type Cy
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Milestone 2 75 Host Gene Expression
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Milestone 2 78 The MAGGIE Project:
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Milestone 2 2. 108 * Presenting aut
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Milestone 2 81 Comprehensive Study
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Milestone 2 83 Development of a Dei
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Milestone 2 limitation, re-enforces
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Milestone 2 86 Single-Molecule Imag
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Milestone 2 TEM at Caltech was used
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Milestone 2 technique and deconvolu
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Milestone 2 122 * Presenting author
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Milestone 2 predicted optimal label
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Milestone 2 126 * Presenting author
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Milestone 2 High-Performance Simula
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Milestone 2 addition to aerobically
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Milestone 2 functionality which are
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Milestone 2 99 Generalized Computer
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Milestone 2 tive function. Our adap
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Milestone 2 103 Genome-Scale Metabo
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Milestone 2 105 Integrated Computat
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Milestone 2 107 Metabolomic Functio
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Milestone 2 challenge of isolating
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Milestone 2 Figure 1. The Sea Urchi
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Milestone 2 provides tools for mult
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Milestone 2 ing to gene expression
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Milestone 2 phylogenetic study of t
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Milestone 2 Additional studies on g
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Milestone 2 static or shaken cultur
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Milestone 2 116 The Bacterial Birth
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Milestone 2 ylated by phospho-NarQ
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Milestone 2 119 Integration of Cont
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Milestone 2 120 High-Resolution Phy
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Milestone 3 Section 1 Computing Inf
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Computing Infrastructure and Educat
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Communication • 172 * Presenting
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Ethical, Legal, and Societal Issues
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Ethical, Legal, and Societal Issues
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Participants Frank Bergmann Keck Gr
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Participants John Glass J. Craig Ve
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Participants Carole Lartigue J. Cra
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Participants Monica Riley Marine Bi
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Participants Sharlene Weatherwax U.
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Web Sites • • • • • •
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Index Chen, Xiaoli 32 Chen, Zhiqian
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Index Klein, David 104 Klingeman, D
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Index Schmutz, Jeremy 3 Schrader, P
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Agencourt Bioscience 19 American Ty
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Joint Meeting - Genomics - U.S. Department of Energy

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