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1. Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi

Author

Larry Watthey, Lisa McDonald, Delwood Richardson, Cheryl Bowman, Bonnie Hatch, Wai Mun Huang, Nanette Palmer, J. Craig Venter, Granger G. Sutton, Robert J. Dodson, Brian Dougherty, J F Tomb, John Quackenbush, Claire Fujii, Matthew D. Cotton, Rebecca A. Clayton, Erin Hickey, Steven L. Salzberg, Teresa Utterback, Janice Weidman, Michelle L. Gwinn, Kevin Roberts, Stacey Garland, Mark Raymond Adams, Claire M. Fraser, Raju Lathigra, Mark S. Hanson, Sherwood R. Casjens, Patricia Artiach, Owen White, René Van Vugt, Anthony R. Kerlavage, Karen A. Ketchum, Jeannine D. Gocayne, Jeremy Peterson, Robert D. Fleischmann, Hamilton O. Smith, and Kurt Horst

Subjects
DNA, Bacterial, DNA Repair, Transcription, Genetic, Molecular Sequence Data, Replication Origin, Genome, Plasmid, Borrelia burgdorferi Group, Antigenic variation, Gene family, Borrelia burgdorferi, Gene, Recombination, Genetic, Genetics, Lyme Disease, Multidisciplinary, biology, Chemotaxis, Membrane Proteins, Biological Transport, Gene Expression Regulation, Bacterial, Chromosomes, Bacterial, Telomere, bacterial infections and mycoses, biology.organism_classification, Protein Biosynthesis, Lyme disease microbiology, Energy Metabolism, Mycoplasma genitalium, Genome, Bacterial, Plasmids
Abstract

The genome of the bacterium Borrelia burgdorferi B31, the aetiologic agent of Lyme disease, contains a linear chromosome of 910,725 base pairs and at least 17 linear and circular plasmids with a combined size of more than 533,000 base pairs. The chromosome contains 853 genes encoding a basic set of proteins for DNA replication, transcription, translation, solute transport and energy metabolism, but, like Mycoplasma genitalium, it contains no genes for cellular biosynthetic reactions. Because B. burgdorferi and M. genitalium are distantly related eubacteria, we suggest that their limited metabolic capacities reflect convergent evolution by gene loss from more metabolically competent progenitors. Of 430 genes on 11 plasmids, most have no known biological function; 39% of plasmid genes are paralogues that form 47 gene families. The biological significance of the multiple plasmid-encoded genes is not clear, although they may be involved in antigenic variation or immune evasion.

Published
1997
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2. Rapid and reliable fluorescent cycle sequencing of double-stranded templates

Author

W. R. McCombie, Michael G. FitzGerald, Jeannine D. Gocayne, C. Heiner, and Jenny M. Kelley

Subjects
Genetics, DNA nanoball sequencing, Massive parallel sequencing, Base Sequence, Molecular Sequence Data, Multiple displacement amplification, DNA, Single-Stranded, Sequence assembly, DNA, Templates, Genetic, Computational biology, Biology, Biochemistry, Fluorescence, DNA sequencing, Sequencing by ligation, DNA sequencer, Endocrinology, Sequencing by hybridization, Cloning, Molecular, Molecular Biology, Plasmids
Abstract

Automated DNA sequencing is an extremely valuable technique which requires very high quality DNA templates to be carried out successfully. While it has been possible to readily produce large numbers of such templates from M13 or other single-stranded vectors for several years, the sequencing of double-stranded DNA templates using the ABI 373 DNA Sequencer has had a considerably lower success rate. We describe how the combination of a new fluorescent, dideoxy sequencing method, called cycle-sequencing, coupled with modifications to template isolation procedures based on Qiagen columns, makes fluorescent sequencing of double-stranded templates a reliable procedure. From a single five milliliter culture enough DNA can be isolated (up to 20 micrograms) to do 4-8 sequencing reactions, each of which yields 400-500 bases of high quality sequence data. These procedures make the routine use of double-stranded DNA templates a viable strategy in automated DNA sequencing projects.

Published
1992
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3. Complementary DNA Sequencing: Expressed Sequence Tags and Human Genome Project

Author

Jeannine D. Gocayne, Mark Raymond Adams, W. Richard McCombie, Mark Dubnick, Jenny M. Kelley, Hong Xiao, Andrew Wu, J. Craig Venter, Carl R. Merril, Bjorn Olde, Anthony R. Kerlavage, Mihael H. Polymeropoulos, and Ruben F. Moreno

Subjects
Genetics, Expressed sequence tag, Multidisciplinary, Base Sequence, Molecular Sequence Data, Brain, Chromosome Mapping, Gene Expression, DNA, Genome project, Biology, Polymerase Chain Reaction, Genome, DNA sequencing, Automation, Multigene Family, Sequence Homology, Nucleic Acid, Complementary DNA, Human Genome Project, Humans, Genomic library, Human genome, Amino Acid Sequence, Gene, Gene Library
Abstract

Automated partial DNA sequencing was conducted on more than 600 randomly selected human brain complementary DNA (cDNA) clones to generate expressed sequence tags (ESTs). ESTs have applications in the discovery of new human genes, mapping of the human genome, and identification of coding regions in genomic sequences. Of the sequences generated, 337 represent new genes, including 48 with significant similarity to genes from other organisms, such as a yeast RNA polymerase II subunit; Drosophila kinesin, Notch, and Enhancer of split; and a murine tyrosine kinase receptor. Forty-six ESTs were mapped to chromosomes after amplification by the polymerase chain reaction. This fast approach to cDNA characterization will facilitate the tagging of most human genes in a few years at a fraction of the cost of complete genomic sequencing, provide new genetic markers, and serve as a resource in diverse biological research fields.

Published
1991
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4. A comparison of whole-genome shotgun-derived mouse chromosome 16 and the human genome

Author

Richard J, Mural, Mark D, Adams, Eugene W, Myers, Hamilton O, Smith, George L Gabor, Miklos, Ron, Wides, Aaron, Halpern, Peter W, Li, Granger G, Sutton, Joe, Nadeau, Steven L, Salzberg, Robert A, Holt, Chinnappa D, Kodira, Fu, Lu, Lin, Chen, Zuoming, Deng, Carlos C, Evangelista, Weiniu, Gan, Thomas J, Heiman, Jiayin, Li, Zhenya, Li, Gennady V, Merkulov, Natalia V, Milshina, Ashwinikumar K, Naik, Rong, Qi, Bixiong Chris, Shue, Aihui, Wang, Jian, Wang, Xin, Wang, Xianghe, Yan, Jane, Ye, Shibu, Yooseph, Qi, Zhao, Liansheng, Zheng, Shiaoping C, Zhu, Kendra, Biddick, Randall, Bolanos, Arthur L, Delcher, Ian M, Dew, Daniel, Fasulo, Michael J, Flanigan, Daniel H, Huson, Saul A, Kravitz, Jason R, Miller, Clark M, Mobarry, Knut, Reinert, Karin A, Remington, Qing, Zhang, Xiangqun H, Zheng, Deborah R, Nusskern, Zhongwu, Lai, Yiding, Lei, Wenyan, Zhong, Alison, Yao, Ping, Guan, Rui-Ru, Ji, Zhiping, Gu, Zhen-Yuan, Wang, Fei, Zhong, Chunlin, Xiao, Chia-Chien, Chiang, Mark, Yandell, Jennifer R, Wortman, Peter G, Amanatides, Suzanne L, Hladun, Eric C, Pratts, Jeffery E, Johnson, Kristina L, Dodson, Kerry J, Woodford, Cheryl A, Evans, Barry, Gropman, Douglas B, Rusch, Eli, Venter, Mei, Wang, Thomas J, Smith, Jarrett T, Houck, Donald E, Tompkins, Charles, Haynes, Debbie, Jacob, Soo H, Chin, David R, Allen, Carl E, Dahlke, Robert, Sanders, Kelvin, Li, Xiangjun, Liu, Alexander A, Levitsky, William H, Majoros, Quan, Chen, Ashley C, Xia, John R, Lopez, Michael T, Donnelly, Matthew H, Newman, Anna, Glodek, Cheryl L, Kraft, Marc, Nodell, Feroze, Ali, Hui-Jin, An, Danita, Baldwin-Pitts, Karen Y, Beeson, Shuang, Cai, Mark, Carnes, Amy, Carver, Parris M, Caulk, Angela, Center, Yen-Hui, Chen, Ming-Lai, Cheng, My D, Coyne, Michelle, Crowder, Steven, Danaher, Lionel B, Davenport, Raymond, Desilets, Susanne M, Dietz, Lisa, Doup, Patrick, Dullaghan, Steven, Ferriera, Carl R, Fosler, Harold C, Gire, Andres, Gluecksmann, Jeannine D, Gocayne, Jonathan, Gray, Brit, Hart, Jason, Haynes, Jeffery, Hoover, Tim, Howland, Chinyere, Ibegwam, Mena, Jalali, David, Johns, Leslie, Kline, Daniel S, Ma, Steven, MacCawley, Anand, Magoon, Felecia, Mann, David, May, Tina C, McIntosh, Somil, Mehta, Linda, Moy, Mee C, Moy, Brian J, Murphy, Sean D, Murphy, Keith A, Nelson, Zubeda, Nuri, Kimberly A, Parker, Alexandre C, Prudhomme, Vinita N, Puri, Hina, Qureshi, John C, Raley, Matthew S, Reardon, Megan A, Regier, Yu-Hui C, Rogers, Deanna L, Romblad, Jakob, Schutz, John L, Scott, Richard, Scott, Cynthia D, Sitter, Michella, Smallwood, Arlan C, Sprague, Erin, Stewart, Renee V, Strong, Ellen, Suh, Karena, Sylvester, Reginald, Thomas, Ni Ni, Tint, Christopher, Tsonis, Gary, Wang, George, Wang, Monica S, Williams, Sherita M, Williams, Sandra M, Windsor, Keriellen, Wolfe, Mitchell M, Wu, Jayshree, Zaveri, Kabir, Chaturvedi, Andrei E, Gabrielian, Zhaoxi, Ke, Jingtao, Sun, Gangadharan, Subramanian, J Craig, Venter, Cynthia M, Pfannkoch, Mary, Barnstead, and Lisa D, Stephenson

Subjects
Genetic Markers, Genome evolution, Mice, Inbred A, Molecular Sequence Data, Genomics, Mice, Inbred Strains, Biology, Genome, Synteny, Chromosomes, Evolution, Molecular, Mice, Species Specificity, Gene density, Animals, Chromosomes, Human, Humans, Conserved Sequence, Genetics, Base Composition, Multidisciplinary, Shotgun sequencing, Genome, Human, Computational Biology, Proteins, Genome project, Sequence Analysis, DNA, Physical Chromosome Mapping, Genes, Mice, Inbred DBA, Human genome, Databases, Nucleic Acid, Sequence Alignment, Reference genome
Abstract

The high degree of similarity between the mouse and human genomes is demonstrated through analysis of the sequence of mouse chromosome 16 (Mmu 16), which was obtained as part of a whole-genome shotgun assembly of the mouse genome. The mouse genome is about 10% smaller than the human genome, owing to a lower repetitive DNA content. Comparison of the structure and protein-coding potential of Mmu 16 with that of the homologous segments of the human genome identifies regions of conserved synteny with human chromosomes (Hsa) 3, 8, 12, 16, 21, and 22. Gene content and order are highly conserved between Mmu 16 and the syntenic blocks of the human genome. Of the 731 predicted genes on Mmu 16, 509 align with orthologs on the corresponding portions of the human genome, 44 are likely paralogous to these genes, and 164 genes have homologs elsewhere in the human genome; there are 14 genes for which we could find no human counterpart.

Published
2002

5. The genome sequence of Drosophila melanogaster

Author

Mark D. Adams, Susan E. Celniker, Robert A. Holt, Cheryl A. Evans, Jeannine D. Gocayne, Peter G. Amanatides, Steven E. Scherer, Peter W. Li, Roger A. Hoskins, Richard F. Galle, Reed A. George, Suzanna E. Lewis, Stephen Richards, Michael Ashburner, Scott N. Henderson, Granger G. Sutton, Jennifer R. Wortman, Mark D. Yandell, Qing Zhang, Lin X. Chen, Rhonda C. Brandon, Yu-Hui C. Rogers, Robert G. Blazej, Mark Champe, Barret D. Pfeiffer, Kenneth H. Wan, Clare Doyle, Evan G. Baxter, Gregg Helt, Catherine R. Nelson, George L. Gabor, null Miklos, Josep F. Abril, Anna Agbayani, Hui-Jin An, Cynthia Andrews-Pfannkoch, Danita Baldwin, Richard M. Ballew, Anand Basu, James Baxendale, Leyla Bayraktaroglu, Ellen M. Beasley, Karen Y. Beeson, P. V. Benos, Benjamin P. Berman, Deepali Bhandari, Slava Bolshakov, Dana Borkova, Michael R. Botchan, John Bouck, Peter Brokstein, Phillipe Brottier, Kenneth C. Burtis, Dana A. Busam, Heather Butler, Edouard Cadieu, Angela Center, Ishwar Chandra, J. Michael Cherry, Simon Cawley, Carl Dahlke, Lionel B. Davenport, Peter Davies, Beatriz de Pablos, Arthur Delcher, Zuoming Deng, Anne Deslattes Mays, Ian Dew, Suzanne M. Dietz, Kristina Dodson, Lisa E. Doup, Michael Downes, Shannon Dugan-Rocha, Boris C. Dunkov, Patrick Dunn, Kenneth J. Durbin, Carlos C. Evangelista, Concepcion Ferraz, Steven Ferriera, Wolfgang Fleischmann, Carl Fosler, Andrei E. Gabrielian, Neha S. Garg, William M. Gelbart, Ken Glasser, Anna Glodek, Fangcheng Gong, J. Harley Gorrell, Zhiping Gu, Ping Guan, Michael Harris, Nomi L. Harris, Damon Harvey, Thomas J. Heiman, Judith R. Hernandez, Jarrett Houck, Damon Hostin, Kathryn A. Houston, Timothy J. Howland, Ming-Hui Wei, Chinyere Ibegwam, Mena Jalali, Francis Kalush, Gary H. Karpen, Zhaoxi Ke, James A. Kennison, Karen A. Ketchum, Bruce E. Kimmel, Chinnappa D. Kodira, Cheryl Kraft, Saul Kravitz, David Kulp, Zhongwu Lai, Paul Lasko, Yiding Lei, Alexander A. Levitsky, Jiayin Li, Zhenya Li, Yong Liang, Xiaoying Lin, Xiangjun Liu, Bettina Mattei, Tina C. McIntosh, Michael P. McLeod, Duncan McPherson, Gennady Merkulov, Natalia V. Milshina, Clark Mobarry, Joe Morris, Ali Moshrefi, Stephen M. Mount, Mee Moy, Brian Murphy, Lee Murphy, Donna M. Muzny, David L. Nelson, David R. Nelson, Keith A. Nelson, Katherine Nixon, Deborah R. Nusskern, Joanne M. Pacleb, Michael Palazzolo, Gjange S. Pittman, Sue Pan, John Pollard, Vinita Puri, Martin G. Reese, Knut Reinert, Karin Remington, Robert D. C. Saunders, Frederick Scheeler, Hua Shen, Bixiang Christopher Shue, Inga Sidén-Kiamos, Michael Simpson, Marian P. Skupski, Tom Smith, Eugene Spier, Allan C. Spradling, Mark Stapleton, Renee Strong, Eric Sun, Robert Svirskas, Cyndee Tector, Russell Turner, Eli Venter, Aihui H. Wang, Xin Wang, Zhen-Yuan Wang, David A. Wassarman, George M. Weinstock, Jean Weissenbach, Sherita M. Williams, Trevor Woodage, Kim C. Worley, David Wu, Song Yang, Q. Alison Yao, Jane Ye, Ru-Fang Yeh, Jayshree S. Zaveri, Ming Zhan, Guangren Zhang, Qi Zhao, Liansheng Zheng, Xiangqun H. Zheng, Fei N. Zhong, Wenyan Zhong, Xiaojun Zhou, Shiaoping Zhu, Xiaohong Zhu, Hamilton O. Smith, Richard A. Gibbs, Eugene W. Myers, Gerald M. Rubin, and J. Craig Venter

Subjects
DNA Replication, Genome evolution, DNA Repair, Transcription, Genetic, Genes, Insect, Computational biology, Biology, Genome, Euchromatin, Contig Mapping, Cytochrome P-450 Enzyme System, Gene density, Heterochromatin, Animals, Cloning, Molecular, Genome size, Gene Library, Whole genome sequencing, Genetics, Bacterial artificial chromosome, Multidisciplinary, Shotgun sequencing, Computational Biology, Nuclear Proteins, Biological Transport, Genome project, Sequence Analysis, DNA, Chromatin, Drosophila melanogaster, Protein Biosynthesis, Insect Proteins
Abstract

The fly Drosophila melanogaster is one of the most intensively studied organisms in biology and serves as a model system for the investigation of many developmental and cellular processes common to higher eukaryotes, including humans. We have determined the nucleotide sequence of nearly all of the ∼120-megabase euchromatic portion of the Drosophila genome using a whole-genome shotgun sequencing strategy supported by extensive clone-based sequence and a high-quality bacterial artificial chromosome physical map. Efforts are under way to close the remaining gaps; however, the sequence is of sufficient accuracy and contiguity to be declared substantially complete and to support an initial analysis of genome structure and preliminary gene annotation and interpretation. The genome encodes ∼13,600 genes, somewhat fewer than the smaller Caenorhabditis elegans genome, but with comparable functional diversity.

Published
2000

6. Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii

Author

Carol J. Bult, Owen White, Gary J. Olsen, Lixin Zhou, Robert D. Fleischmann, Granger G. Sutton, Judith A. Blake, Lisa M. FitzGerald, Rebecca A. Clayton, Jeannine D. Gocayne, Anthony R. Kerlavage, Brian A. Dougherty, Jean-Francois Tomb, Mark D. Adams, Claudia I. Reich, Ross Overbeek, Ewen F. Kirkness, Keith G. Weinstock, Joseph M. Merrick, Anna Glodek, John L. Scott, Neil S. M. Geoghagen, Janice F. Weidman, Joyce L. Fuhrmann, Dave Nguyen, Teresa R. Utterback, Jenny M. Kelley, Jeremy D. Peterson, Paul W. Sadow, Michael C. Hanna, Matthew D. Cotton, Kevin M. Roberts, Margaret A. Hurst, Brian P. Kaine, Mark Borodovsky, Hans-Peter Klenk, Claire M. Fraser, Hamilton O. Smith, Carl R. Woese, and J. Craig Venter

Subjects
DNA Replication, DNA, Bacterial, Methanococcus, Databases, Factual, Transcription, Genetic, Sequence analysis, Molecular Sequence Data, Biology, Genome, Bacterial Proteins, Amino Acid Sequence, Repeated sequence, Genetics, Whole genome sequencing, Base Composition, Multidisciplinary, Base Sequence, Nucleic acid sequence, Methanocaldococcus jannaschii, Chromosome Mapping, Methanococcus maripaludis, Biological Transport, Sequence Analysis, DNA, Carbon Dioxide, Chromosomes, Bacterial, biology.organism_classification, Genes, Bacterial, Protein Biosynthesis, Energy Metabolism, Methane, Genome, Bacterial, Hydrogen
Abstract

The complete 1.66-megabase pair genome sequence of an autotrophic archaeon, Methanococcus jannaschii, and its 58- and 16-kilobase pair extrachromosomal elements have been determined by whole-genome random sequencing. A total of 1738 predicted protein-coding genes were identified; however, only a minority of these (38 percent) could be assigned a putative cellular role with high confidence. Although the majority of genes related to energy production, cell division, and metabolism in M. jannaschii are most similar to those found in Bacteria, most of the genes involved in transcription, translation, and replication in M. jannaschii are more similar to those found in Eukaryotes.

Published
1996

7. A model for high-throughput automated DNA sequencing and analysis core facilities

Author

Mark Raymond Adams, Jenny M. Kelley, Claire M. Fraser, J. Craig Venter, Jeannine D. Gocayne, Chris Fields, and Anthony R. Kerlavage

Subjects
Quantitative Biology::Biomolecules, Multidisciplinary, Computer science, Nucleic acid sequence, Academies and Institutes, Computational biology, Sequence Analysis, DNA, Bioinformatics, Quantitative Biology::Genomics, DNA sequencing, United States, chemistry.chemical_compound, Automation, chemistry, National Institutes of Health (U.S.), Animals, Humans, Laboratories, Gene, Throughput (business), DNA, Information Systems
Abstract

Large-scale DNA sequencing and analysis is providing important molecular information on complex biological systems.

Published
1994

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