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8 results on '"Jeannine D, Gocayne"'

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. More on the sequencing of the human genome

Author

J. Craig Venter, Mark D. Adams, Eugene W. Myers, Peter W. Li, Richard J. Mural, Granger G. Sutton, Hamilton O. Smith, Mark Yandell, Cheryl A. Evans, Robert A. Holt, Jeannine D. Gocayne, Peter Amanatides, Richard M. Ballew, Daniel H. Huson, Jennifer Russo Wortman, Qing Zhang, Chinnappa D. Kodira, Xiangqun H. Zheng, Lin Chen, Marian Skupski, Gangadharan Subramanian, Paul D. Thomas, Jinghui Zhang, George L. Gabor Miklos, Catherine Nelson, Samuel Broder, Andrew G. Clark, Joe Nadeau, Victor A. McKusick, Norton Zinder, Arnold J. Levine, Richard J. Roberts, Mel Simon, Carolyn Slayman, Michael Hunkapiller, Randall Bolanos, Arthur Delcher, Ian Dew, Daniel Fasulo, Michael Flanigan, Liliana Florea, Aaron Halpern, Sridhar Hannenhalli, Saul Kravitz, Samuel Levy, Clark Mobarry, Knut Reinert, Karin Remington, Jane Abu-Threideh, Ellen Beasley, Kendra Biddick, Vivien Bonazzi, Rhonda Brandon, Michele Cargill, Ishwar Chandramouliswaran, Rosane Charlab, Kabir Chaturvedi, Zuoming Deng, Valentina Di Francesco, Patrick Dunn, Karen Eilbeck, Carlos Evangelista, Andrei E. Gabrielian, Weiniu Gan, Wangmao Ge, Fangcheng Gong, Zhiping Gu, Ping Guan, Thomas J. Heiman, Maureen E. Higgins, Rui-Ru Ji, Zhaoxi Ke, Karen A. Ketchum, Zhongwu Lai, Yiding Lei, Zhenya Li, Jiayin Li, Yong Liang, Xiaoying Lin, Fu Lu, Gennady V. Merkulov, Natalia Milshina, Helen M. Moore, Ashwinikumar K Naik, Vaibhav A. Narayan, Beena Neelam, Deborah Nusskern, Douglas B. Rusch, Steven Salzberg, Wei Shao, Bixiong Shue, Jingtao Sun, Zhen Yuan Wang, Aihui Wang, Xin Wang, Jian Wang, Ming-Hui Wei, Ron Wides, Chunlin Xiao, Chunhua Yan, Alison Yao, Jane Ye, Ming Zhan, Weiqing Zhang, Hongyu Zhang, Qi Zhao, Liansheng Zheng, Fei Zhong, Wenyan Zhong, Shiaoping C. Zhu, Shaying Zhao, Dennis Gilbert, Suzanna Baumhueter, Gene Spier, Christine Carter, Anibal Cravchik, Trevor Woodage, Feroze Ali, Huijin An, Aderonke Awe, Danita Baldwin, Holly Baden, Mary Barnstead, Ian Barrow, Karen Beeson, Dana Busam, Amy Carver, Angela Center, Ming Lai Cheng, Liz Curry, Steve Danaher, Lionel Davenport, Raymond Desilets, Susanne Dietz, Kristina Dodson, Lisa Doup, Steven Ferriera, Neha Garg, Andres Gluecksmann, Brit Hart, Jason Haynes, Charles Haynes, Cheryl Heiner, Suzanne Hladun, Damon Hostin, Jarrett Houck, Timothy Howland, Chinyere Ibegwam, Jeffery Johnson, Francis Kalush, Lesley Kline, Shashi Koduru, Amy Love, Felecia Mann, David May, Steven McCawley, Tina McIntosh, Ivy McMullen, Mee Moy, Linda Moy, Brian Murphy, Keith Nelson, Cynthia Pfannkoch, Eric Pratts, Vinita Puri, Hina Qureshi, Matthew Reardon, Robert Rodriguez, Yu-Hui Rogers, Deanna Romblad, Bob Ruhfel, Richard Scott, Cynthia Sitter, Michelle Smallwood, Erin Stewart, Renee Strong, Ellen Suh, Reginald Thomas, Ni Ni Tint, Sukyee Tse, Claire Vech, Gary Wang, Jeremy Wetter, Sherita Williams, Monica Williams, Sandra Windsor, Emily Winn-Deen, Keriellen Wolfe, Jayshree Zaveri, Karena Zaveri, Josep F. Abril, Roderic Guigó, Michael J. Campbell, Kimmen V. Sjolander, Brian Karlak, Anish Kejariwal, Huaiyu Mi, Betty Lazareva, Thomas Hatton, Apurva Narechania, Karen Diemer, Anushya Muruganujan, Nan Guo, Shinji Sato, Vineet Bafna, Sorin Istrail, Ross Lippert, Russell Schwartz, Brian Walenz, Shibu Yooseph, David Allen, Anand Basu, James Baxendale, Louis Blick, Marcelo Caminha, John Carnes-Stine, Parris Caulk, Yen-Hui Chiang, My Coyne, Carl Dahlke, Anne Deslattes Mays, Maria Dombroski, Michael Donnelly, Dale Ely, Shiva Esparham, Carl Fosler, Harold Gire, Stephen Glanowski, Kenneth Glasser, Anna Glodek, Mark Gorokhov, Ken Graham, Barry Gropman, Michael Harris, Jeremy Heil, Scott Henderson, Jeffrey Hoover, Donald Jennings, Catherine Jordan, James Jordan, John Kasha, Leonid Kagan, Cheryl Kraft, Alexander Levitsky, Mark Lewis, Xiangjun Liu, John Lopez, Daniel Ma, William Majoros, Joe McDaniel, Sean Murphy, Matthew Newman, Trung Nguyen, Ngoc Nguyen, Marc Nodell, Sue Pan, Jim Peck, Marshall Peterson, William Rowe, Robert Sanders, John Scott, Michael Simpson, Thomas Smith, Arlan Sprague, Timothy Stockwell, Russell Turner, Eli Venter, Mei Wang, Meiyuan Wen, David Wu, Mitchell Wu, Ashley Xia, Ali Zandieh, and Xiaohong Zhu

Subjects
Male, Cancer genome sequencing, Chromosomes, Artificial, Bacterial, Databases, Factual, Clinical Biochemistry, Genome, Gene Duplication, Databases, Genetic, Human Genome Project, Genetics, Multidisciplinary, Chromosome Mapping, Exons, Genomics, Genome project, Physical Chromosome Mapping, Phenotype, Genetic Techniques, Perspective, DNA, Intergenic, Female, Algorithms, Pseudogenes, Personal genomics, Genome evolution, Retroelements, Hybrid genome assembly, Biology, ENCODE, Polymorphism, Single Nucleotide, Evolution, Molecular, Sequence-tagged site, Species Specificity, Gene density, Consensus Sequence, Animals, Humans, Genome size, Repetitive Sequences, Nucleic Acid, Whole genome sequencing, Comparative genomics, Genome, Human, Biochemistry (medical), Computational Biology, Genetic Variation, Proteins, Sequence Analysis, DNA, Introns, Chromosome Banding, Genes, CpG Islands, Reference genome
Abstract

A 2.91-billion base pair (bp) consensus sequence of the euchromatic portion of the human genome was generated by the whole-genome shotgun sequencing method. The 14.8-billion bp DNA sequence was generated over 9 months from 27,271,853 high-quality sequence reads (5.11-fold coverage of the genome) from both ends of plasmid clones made from the DNA of five individuals. Two assembly strategies—a whole-genome assembly and a regional chromosome assembly—were used, each combining sequence data from Celera and the publicly funded genome effort. The public data were shredded into 550-bp segments to create a 2.9-fold coverage of those genome regions that had been sequenced, without including biases inherent in the cloning and assembly procedure used by the publicly funded group. This brought the effective coverage in the assemblies to eightfold, reducing the number and size of gaps in the final assembly over what would be obtained with 5.11-fold coverage. The two assembly strategies yielded very similar results that largely agree with independent mapping data. The assemblies effectively cover the euchromatic regions of the human chromosomes. More than 90% of the genome is in scaffold assemblies of 100,000 bp or more, and 25% of the genome is in scaffolds of 10 million bp or larger. Analysis of the genome sequence revealed 26,588 protein-encoding transcripts for which there was strong corroborating evidence and an additional ∼12,000 computationally derived genes with mouse matches or other weak supporting evidence. Although gene-dense clusters are obvious, almost half the genes are dispersed in low G+C sequence separated by large tracts of apparently noncoding sequence. Only 1.1% of the genome is spanned by exons, whereas 24% is in introns, with 75% of the genome being intergenic DNA. Duplications of segmental blocks, ranging in size up to chromosomal lengths, are abundant throughout the genome and reveal a complex evolutionary history. Comparative genomic analysis indicates vertebrate expansions of genes associated with neuronal function, with tissue-specific developmental regulation, and with the hemostasis and immune systems. DNA sequence comparisons between the consensus sequence and publicly funded genome data provided locations of 2.1 million single-nucleotide polymorphisms (SNPs). A random pair of human haploid genomes differed at a rate of 1 bp per 1250 on average, but there was marked heterogeneity in the level of polymorphism across the genome. Less than 1% of all SNPs resulted in variation in proteins, but the task of determining which SNPs have functional consequences remains an open challenge.

Published
2003
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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. The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus

Author

Anna Glodek, Keith McKenney, Lixin Zhou, Nikos C. Kyrpides, David E. Graham, Mark Raymond Adams, Hamilton O. Smith, Karen A. Ketchum, Brian P. Kaine, Cheryl Bowman, Matthew D. Cotton, Rebecca A. Clayton, Karen E. Nelson, Sean M. Sykes, Leslie Klis McNeil, Scott N. Peterson, Janice Weidman, Claudia I. Reich, Tracy Spriggs, Robert D. Fleischmann, Granger G. Sutton, Stacey Garland, Ewen F. Kirkness, Paul W. Sadow, Jonathan H. Badger, Jean-Francois Tomb, Robert J. Dodson, Teresa Utterback, Delwood Richardson, Tanya Mason, Claire Fujii, Brendan J. Loftus, Steven R. Gill, Claire M. Fraser, Brian Dougherty, Michelle Gwinn, John Quackenbush, Lisa McDonald, Patricia Artiach, Owen White, Gary J. Olsen, Carl R. Woese, Jeannine D. Gocayne, Kurt P. D'Andrea, Hans-Peter Klenk, Jeremy Peterson, J. Craig Venter, Ross Overbeek, Norman H. Lee, Anthony R. Kerlavage, and Erin Hickey

Subjects
Genetics, DNA, Bacterial, Methanococcus, Multidisciplinary, Genome, biology, Base Sequence, Transcription, Genetic, Molecular Sequence Data, Archaeoglobus fulgidus, Nucleic acid sequence, Gene Expression Regulation, Bacterial, biology.organism_classification, Genes, Archaeal, Protein Biosynthesis, Archaeoglobus, ORFS, Energy Metabolism, Gene, Cell Division, Genomic organization
Abstract

Archaeoglobus fulgidus is the first sulphur-metabolizing organism to have its genome sequence determined. Its genome of 2,178,400 base pairs contains 2,436 open reading frames (ORFs). The information processing systems and the biosynthetic pathways for essential components (nucleotides, amino acids and cofactors) have extensive correlation with their counterparts in the archaeon Methanococcus jannaschii. The genomes of these two Archaea indicate dramatic differences in the way these organisms sense their environment, perform regulatory and transport functions, and gain energy. In contrast to M. jannaschii, A. fulgidus has fewer restriction-modification systems, and none of its genes appears to contain inteins. A quarter (651 ORFs) of the A. fulgidus genome encodes functionally uncharacterized yet conserved proteins, two-thirds of which are shared with M. jannaschii (428 ORFs). Another quarter of the genome encodes new proteins indicating substantial archaeal gene diversity.

Published
1997

7. 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

8. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd

Author

Robert D. Fleischmann, Mark D. Adams, Owen White, Rebecca A. Clayton, Ewen F. Kirkness, Anthony R. Kerlavage, Carol J. Bult, Jean-Francois Tomb, Brian A. Dougherty, Joseph M. Merrick, Keith McKenney, Granger Sutton, Will FitzHugh, Chris Fields, Jeannine D. Gocayne, John Scott, Robert Shirley, Li-lng Liu, Anna Glodek, Jenny M. Kelley, Janice F. Weidman, Cheryl A. Phillips, Tracy Spriggs, Eva Hedblom, Matthew D. Cotton, Teresa R. Utterback, Michael C. Hanna, David T. Nguyen, Deborah M. Saudek, Rhonda C. Brandon, Leah D. Fine, Janice L. Fritchman, Joyce L. Fuhrmann, N. S. M. Geoghagen, Cheryl L. Gnehm, Lisa A. McDonald, Keith V. Small, Claire M. Fraser, Hamilton O. Smith, and J. Craig Venter

Subjects
DNA, Bacterial, Cancer genome sequencing, Databases, Factual, Molecular Sequence Data, Biology, Genome, Sequence-tagged site, Bacterial Proteins, Operon, Cloning, Molecular, Exome sequencing, Repetitive Sequences, Nucleic Acid, Genetics, Whole genome sequencing, Base Composition, Multidisciplinary, Base Sequence, Chromosome Mapping, Sequence Analysis, DNA, Genome project, Chromosomes, Bacterial, Accession number (bioinformatics), Haemophilus influenzae, RNA, Bacterial, Genes, Bacterial, RNA, Ribosomal, Costs and Cost Analysis, Genome, Bacterial, Software, Reference genome
Abstract

An approach for genome analysis based on sequencing and assembly of unselected pieces of DNA from the whole chromosome has been applied to obtain the complete nucleotide sequence (1,830,137 base pairs) of the genome from the bacterium Haemophilus influenzae Rd. This approach eliminates the need for initial mapping efforts and is therefore applicable to the vast array of microbial species for which genome maps are unavailable. The H. influenzae Rd genome sequence (Genome Sequence DataBase accession number L42023) represents the only complete genome sequence from a free-living organism.

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