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1. Complete genome sequence of Neisseria meningitidis serogroup B strain MC58

Author

William C. Nelson, Debbie S. Parksey, Michelle L. Gwinn, Jonathan A. Eisen, John F. Heidelberg, J. Craig Venter, Karen A. Ketchum, Robert D. Fleischmann, Vincenzo Scarlato, John Gill, Robert J. Dodson, Haiying Qin, Hervé Tettelin, Robert T. DeBoy, Brian Dougherty, E. Richard Moxon, Jessica Vamathevan, Henry Cittone, Steven L. Salzberg, Nigel J. Saunders, Karen E. Nelson, Anne Ciecko, Li Sun, Hamilton O. Smith, Guido Grandi, Jeremy Peterson, Tanya Mason, Emily B. Clark, Owen White, Derek W. Hood, Claire M. Fraser, Erin Hickey, Eric Blair, T. Utterback, Vega Masignani, Alex C. Jeffries, John F. Peden, Daniel H. Haft, Matthew D. Cotton, Hoda Khouri, Mariagrazia Pizza, Rino Rappuoli, Tettelin H., Saunders N.J., Heidelberg J., Jeffries A.C., Nelson K.E., Eisen J.A., Ketchum K.A., Hood D.W., Peden J.F., Dodson R.J., Nelson W.C., Gwinn M.L., DeBoy R., Peterson J.D., Hickey E.K., Haft D.H., Salzberg S.L., White O., Fleischmann R.D., Dougherty B.A., Mason T., Ciecko A., Parksey D.S., Blair E., Cittone H., Clark E.B., Cotton M.D., Utterback T.R., Khouri H., Qin H., Vamathevan J., Gill J., Scarlato V., Masignani V., Pizza M., Grandi G., Sun L., Smith H.O., Fraser C.M., Moxon E.R., Rappuoli R., and Craig Venter J.

Subjects
Sequence analysis, genome sequence, genetic islands, phase variation, Molecular Sequence Data, Virulence, Bacteremia, Meningitis, Meningococcal, Neisseria meningitidis, medicine.disease_cause, Genome, Microbiology, Evolution, Molecular, Open Reading Frames, Bacterial Proteins, Operon, medicine, Antigenic variation, Humans, Serotyping, Gene, Bacterial Capsules, Phylogeny, Recombination, Genetic, Genetics, Phase variation, Antigens, Bacterial, Multidisciplinary, biology, Sequence Analysis, DNA, biology.organism_classification, Antigenic Variation, Meningococcal Infections, Fimbriae, Bacterial, Mutation, Neisseria lactamica, DNA Transposable Elements, Transformation, Bacterial, Genome, Bacterial
Abstract

The 2,272,351–base pair genome ofNeisseria meningitidisstrain MC58 (serogroup B), a causative agent of meningitis and septicemia, contains 2158 predicted coding regions, 1158 (53.7%) of which were assigned a biological role. Three major islands of horizontal DNA transfer were identified; two of these contain genes encoding proteins involved in pathogenicity, and the third island contains coding sequences only for hypothetical proteins. Insights into the commensal and virulence behavior ofN. meningitidiscan be gleaned from the genome, in which sequences for structural proteins of the pilus are clustered and several coding regions unique to serogroup B capsular polysaccharide synthesis can be identified. Finally,N. meningitidiscontains more genes that undergo phase variation than any pathogen studied to date, a mechanism that controls their expression and contributes to the evasion of the host immune system.

Published
2016
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2. 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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3. The complete genome sequence of the gastric pathogen Helicobacter pylori

Author

Granger G. Sutton, Teresa Utterback, Hans-Peter Klenk, Anthony R. Kerlavage, Robert D. Fleischmann, Delwood Richardson, Norman H. Lee, Douglas E. Berg, Brian Dougherty, John Quackenbush, J. Craig Venter, Erik Wallin, Claire Fujii, Rebecca A. Clayton, Jean-F. Tomb, Cheryl Bowman, Scott N. Peterson, Larry Watthey, William S. Hayes, Jeanine D. Gocayne, Anna Glodek, Karen A. Ketchum, Lisa M. Fitzegerald, Keith McKenney, J. Weidman, Matthew D. Cotton, Jeremy Peterson, Mark Raymond Adams, Karen E. Nelson, Erin Hickey, Hamilton O. Smith, Peter D. Karp, Owen White, Ewen F. Kirkness, Lixin Zhou, Claire M. Fraser, Mark Borodovsky, Robert J. Dodson, Brendan J. Loftus, Jenny M. Kelley, Steven R. Gill, and Hanif Khalak

Subjects
DNA, Bacterial, DNA Repair, Transcription, Genetic, Sequence analysis, Molecular Sequence Data, Biology, Genome, Bacterial Adhesion, chemistry.chemical_compound, Bacterial Proteins, Antigenic variation, Gene, Genomic organization, Recombination, Genetic, Genetics, Multidisciplinary, Base Sequence, Helicobacter pylori, Virulence, Nucleic acid sequence, Gene Expression Regulation, Bacterial, Hydrogen-Ion Concentration, Antigenic Variation, Biological Evolution, chemistry, Protein Biosynthesis, Bacterial outer membrane, Cell Division, Genome, Bacterial, DNA
Abstract

Helicobacter pylori, strain 26695, has a circular genome of 1,667,867 base pairs and 1,590 predicted coding sequences. Sequence analysis indicates that H. pylori has well-developed systems for motility, for scavenging iron, and for DNA restriction and modification. Many putative adhesins, lipoproteins and other outer membrane proteins were identified, underscoring the potential complexity of host-pathogen interaction. Based on the large number of sequence-related genes encoding outer membrane proteins and the presence of homopolymeric tracts and dinucleotide repeats in coding sequences, H. pylori, like several other mucosal pathogens, probably uses recombination and slipped-strand mispairing within repeats as mechanisms for antigenic variation and adaptive evolution. Consistent with its restricted niche, H. pylori has a few regulatory networks, and a limited metabolic repertoire and biosynthetic capacity. Its survival in acid conditions depends, in part, on its ability to establish a positive inside-membrane potential in low pH.

Published
1997
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4. Complete genome sequence of Treponema pallidum, the syphilis spirochete

Author

Lisa McDonald, George M. Weinstock, Monjula Chidambaram, Claire M. Fraser, Teresa Utterback, Janice Weidman, Michelle L. Gwinn, Patricia Artiach, Owen White, Jerrilyn K. Howell, Erica Sodergren, Stacey Garland, Granger G. Sutton, Matthew D. Cotton, Mina Sandusky, Robert J. Dodson, Claire Fujii, Steven L. Salzberg, Delwood Richardson, Kevin Roberts, Bonnie Hatch, Karen A. Ketchum, Steven J. Norris, Rebecca A. Clayton, Cheryl Bowman, Michael P. McLeod, Hamilton O. Smith, J. Craig Venter, Kurt Horst, Hanif Khalak, Jeremy Peterson, Erin Hickey, and John M. Hardham

Subjects
DNA Replication, DNA Repair, Transcription, Genetic, Sequence analysis, Lipoproteins, Movement, Molecular Sequence Data, Replication Origin, Genome, Microbiology, Open Reading Frames, Oxygen Consumption, Bacterial Proteins, Borrelia burgdorferi Group, Genes, Regulator, Treponema pallidum, Borrelia burgdorferi, Gene, Genomic organization, Genetics, Whole genome sequencing, Recombination, Genetic, Multidisciplinary, Treponema, biology, Base Sequence, Nucleic acid sequence, Membrane Proteins, DNA Restriction Enzymes, Sequence Analysis, DNA, biology.organism_classification, Genes, Bacterial, Protein Biosynthesis, Carrier Proteins, Energy Metabolism, Genome, Bacterial, Heat-Shock Response
Abstract

The complete genome sequence of Treponema pallidum was determined and shown to be 1,138,006 base pairs containing 1041 predicted coding sequences (open reading frames). Systems for DNA replication, transcription, translation, and repair are intact, but catabolic and biosynthetic activities are minimized. The number of identifiable transporters is small, and no phosphoenolpyruvate:phosphotransferase carbohydrate transporters were found. Potential virulence factors include a family of 12 potential membrane proteins and several putative hemolysins. Comparison of the T. pallidum genome sequence with that of another pathogenic spirochete, Borrelia burgdorferi , the agent of Lyme disease, identified unique and common genes and substantiates the considerable diversity observed among pathogenic spirochetes.

Published
1998

5. 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

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. Erratum: The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus

Author

Lixin Zhou, C. Fujli, Norman H. Lee, A. Glodek, Anthony R. Kerlavage, Gary J. Olsen, P. W. Sadow, Matthew D. Cotton, Cheryl Bowman, Nikos C. Kyrpides, Jeannine D. Gocayne, Tanya Mason, Jeremy Peterson, Keith McKenney, Rebecca A. Clayton, Brendan J. Loftus, Mark Raymond Adams, Lisa McDonald, J F Tomb, Ross Overbeek, C. R. Woese, Erin Hickey, Karen E. Nelson, Claudia I. Reich, David E. Graham, Hamilton O. Smith, T. Spriggs, Hans-Peter Klenk, Sean M. Sykes, Stacey Garland, Ewen F. Kirkness, Leslie Klis McNeil, Jonathan H. Badger, Claire M. Fraser, Steven R. Gill, Patricia Artiach, Scott N. Peterson, Delwood Richardson, J C Venter, Brian Dougherty, J. F. Weldman, John Quackenbush, Michelle L. Gwinn, Robert D. Fleischmann, K. A. Ketchum, Owen White, Brian P. Kaine, R. J. Dodaon, T. Utterback, K. P. D'Andrea, and Granger G. Sutton

Subjects
Whole genome sequencing, Multidisciplinary, Archaeoglobus fulgidus, Computational biology, Biology, Erratum
Published
1998

8. Erratum: The complete genome sequence of the gastric pathogen Helicobacter pylori

Author

Jean-F. Tomb, Owen White, Anthony R. Kerlavage, Rebecca A. Clayton, Granger G. Sutton, Robert D. Fleischmann, Karen A. Ketchum, Hans Peter Klenk, Steven Gill, Brian A. Dougherty, Karen Nelson, John Quackenbush, Lixin Zhou, Ewen F. Kirkness, Scott Peterson, Brendan Loftus, Delwood Richardson, Robert Dodson, Hanif G. Khalak, Anna Glodek, Keith McKenney, Lisa M. Fitzegerald, Norman Lee, Mark D. Adams, Erin K. Hickey, Douglas E. Berg, Jeanine D. Gocayne, Teresa R. Utterback, Jeremy D. Peterson, Jenny M. Kelley, Matthew D. Cotton, Janice M. Weidman, Claire Fujii, Cheryl Bowman, Larry Watthey, Erik Wallin, William S. Hayes, Mark Borodovsky, Peter D. Karp, Hamilton O. Smith, Claire M. Fraser, and J. Craig Venter

Subjects
Whole genome sequencing, Multidisciplinary, Biology, Helicobacter pylori, biology.organism_classification, Pathogen, Virology
Published
1997
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9. Evidence for lateral gene transfer between Archaea and Bacteria from genome sequence of Thermotoga maritima

Author

Cheryl Phillips, Claire M. Fraser, Joel A. Malek, Granger G. Sutton, Jeremy Peterson, Steven R. Gill, Owen White, Matthew S. Pratt, Ashley M. Stewart, Steven L. Salzberg, Teresa Utterback, Jonathan A. Eisen, Erin Hickey, Robert J. Dodson, Karen A. Ketchum, Lisa McDonald, Katja D. Linher, John F. Heidelberg, Rebecca A. Clayton, Robert D. Fleischmann, Delwood Richardson, Daniel H. Haft, Karen E. Nelson, Matthew D. Cotton, Hamilton O. Smith, J. Craig Venter, William C. Nelson, Mina M. Garrett, and Michelle L. Gwinn

Subjects
DNA, Bacterial, Transcription, Genetic, Molecular Sequence Data, Genome, Genes, Archaeal, Open Reading Frames, Bacterial Proteins, Thermotoga maritima, Gene, Phylogeny, Genetics, Recombination, Genetic, Multidisciplinary, biology, Thermophile, Genetic transfer, Sequence Analysis, DNA, Thermotoga, biology.organism_classification, Horizontal gene transfer in evolution, Archaea, Multigene Family, Protein Biosynthesis, bacteria, Transformation, Bacterial, Thermotoga neapolitana, Genome, Bacterial
Abstract

The 1,860,725-base-pair genome of Thermotoga maritima MSB8 contains 1,877 predicted coding regions, 1,014 (54%) of which have functional assignments and 863 (46%) of which are of unknown function. Genome analysis reveals numerous pathways involved in degradation of sugars and plant polysaccharides, and 108 genes that have orthologues only in the genomes of other thermophilic Eubacteria and Archaea. Of the Eubacteria sequenced to date, T. maritima has the highest percentage (24%) of genes that are most similar to archaeal genes. Eighty-one archaeal-like genes are clustered in 15 regions of the T. maritima genome that range in size from 4 to 20 kilobases. Conservation of gene order between T. maritima and Archaea in many of the clustered regions suggests that lateral gene transfer may have occurred between thermophilic Eubacteria and Archaea.

10. 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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