Journal ArticleDOI
Optimized multiplex PCR: efficiently closing a whole-genome shotgun sequencing project.
TLDR
The pipette optimized multiplex PCR method has been employed in the final phases of closing the Streptococcus pneumoniae genome sequence, with excellent results.About:
This article is published in Genomics.The article was published on 1999-12-15. It has received 141 citations till now. The article focuses on the topics: Shotgun sequencing & In silico PCR.read more
Citations
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Journal ArticleDOI
Complete Genome Sequence of a Virulent Isolate of Streptococcus pneumoniae
Hervé Tettelin,Karen E. Nelson,Ian T. Paulsen,Jonathan A. Eisen,Timothy D. Read,Scott N. Peterson,John F. Heidelberg,Robert T. DeBoy,Daniel H. Haft,Robert J. Dodson,Anthony S. Durkin,Michelle L. Gwinn,James F. Kolonay,William C. Nelson,Jeremy Peterson,Lowell Umayam,Owen White,Steven L. Salzberg,Matthew R. Lewis,Diana Radune,Erik Holtzapple,Hoda Khouri,Alex M. Wolf,T. Utterback,Cheryl L. Hansen,Lisa McDonald,Tamara Feldblyum,Samuel V. Angiuoli,T. Dickinson,Erin Hickey,Ingeborg Holt,Brendan J. Loftus,Fan Yang,Hamilton O. Smith,J. C. Venter,Brian Dougherty,Donald A. Morrison,S. K. Hollingshead,Claire M. Fraser +38 more
TL;DR: A motif identified within the signal peptide of proteins is potentially involved in targeting these proteins to the cell surface of low–guanine/cytosine Gram-positive species.
Journal ArticleDOI
Phylogenomics of the Reproductive Parasite Wolbachia pipientis wMel: A Streamlined Genome Overrun by Mobile Genetic Elements
Martin Wu,Ling V. Sun,Jessica Vamathevan,Markus Riegler,Robert T. DeBoy,Jeremy C. Brownlie,Elizabeth A. McGraw,William Martin,Christian Esser,Nahal Ahmadinejad,Christian Wiegand,Ramana Madupu,Maureen J. Beanan,Lauren M. Brinkac,Sean C. Daugherty,A. Scott Durkin,James F. Kolonay,William C. Nelson,Yasmin Ali Mohamoud,Perris Lee,Kristi Berry,M. Brook Young,Teresa Utterback,Janice Weidman,William C. Nierman,Ian T. Paulsen,Karen E. Nelson,Hervé Tettelin,Scott Leslie O'Neill,Scott Leslie O'Neill,Jonathan A. Eisen +30 more
TL;DR: Genetic analysis of the wMel genome further supports the hypothesis that mitochondria share a common ancestor with the α-Proteobacteria, but shows little support for the grouping of mitochondria with species in the order Rickettsiales.
Journal ArticleDOI
Genome sequence of the dissimilatory metal ion-reducing bacterium Shewanella oneidensis.
John F. Heidelberg,Ian T. Paulsen,Karen E. Nelson,Eric Gaidos,Eric Gaidos,William C. Nelson,Timothy D. Read,Jonathan A. Eisen,Rekha Seshadri,Naomi L. Ward,Barbara A. Methé,Rebecca A. Clayton,Terry E. Meyer,A. I. Tsapin,James Scott,Maureen J. Beanan,Lauren M. Brinkac,Sean C. Daugherty,Robert T. DeBoy,Robert J. Dodson,A. Scott Durkin,Daniel H. Haft,James F. Kolonay,Ramana Madupu,Jeremy Peterson,Lowell Umayam,Owen White,Alex M. Wolf,Jessica Vamathevan,Janice Weidman,Marjorie Impraim,K. Lee,Kristy Berry,Chris Lee,Jacob L. Mueller,Hoda Khouri,John Gill,T. Utterback,Lisa McDonald,Tamara Feldblyum,Hamilton O. Smith,J. Craig Venter,Kenneth H. Nealson,Kenneth H. Nealson,Claire M. Fraser +44 more
TL;DR: This genome sequence represents a critical step in the elucidation of the pathways for reduction (and bioremediation) of pollutants such as uranium (U) and chromium (Cr), and offers a starting point for defining this organism's complex electron transport systems and metal ion–reducing capabilities.
Journal ArticleDOI
Three Genomes from the Phylum Acidobacteria Provide Insight into the Lifestyles of These Microorganisms in Soils
Naomi L. Ward,Jean F. Challacombe,Jean F. Challacombe,Peter H. Janssen,Peter H. Janssen,Bernard Henrissat,Pedro M. Coutinho,Martin Wu,Gary Xie,Gary Xie,Daniel H. Haft,Michelle Sait,Jonathan H. Badger,Ravi D. Barabote,Ravi D. Barabote,Brent Bradley,Thomas Brettin,Thomas Brettin,Lauren M. Brinkac,David Bruce,David Bruce,Todd Creasy,Sean C. Daugherty,Tanja M. Davidsen,Robert T. DeBoy,J. Chris Detter,J. Chris Detter,Robert J. Dodson,A. Scott Durkin,Anuradha Ganapathy,Michelle Gwinn-Giglio,Cliff Han,Cliff Han,Hoda Khouri,Hajnalka Kiss,Hajnalka Kiss,Sagar Kothari,Ramana Madupu,Karen E. Nelson,William C. Nelson,Ian T. Paulsen,Kevin Penn,Qinghu Ren,M. J. Rosovitz,Jeremy D. Selengut,Susmita Shrivastava,Steven A. Sullivan,Roxanne Tapia,Roxanne Tapia,L. Sue Thompson,L. Sue Thompson,Kisha Watkins,Qi Yang,Chunhui Yu,Nikhat Zafar,Liwei Zhou,Cheryl R. Kuske +56 more
TL;DR: Combining the genomic evidence with available culture traits, it is postulate that cells of these isolates are long-lived, divide slowly, exhibit slow metabolic rates under low-nutrient conditions, and are well equipped to tolerate fluctuations in soil hydration.
Journal ArticleDOI
The Genome of M. Acetivorans Reveals Extensive Metabolic and Physiological Diversity
James E. Galagan,Chad Nusbaum,Alice Roy,Matthew G. Endrizzi,Matthew G. Endrizzi,Matthew G. Endrizzi,Pendexter Macdonald,Pendexter Macdonald,Pendexter Macdonald,William Fitzhugh,Sarah E. Calvo,Reinhard Engels,Serge Smirnov,Deven Atnoor,Adam Brown,Nicole R. Allen,Nicole R. Allen,Nicole R. Allen,Jerome Naylor,Nicole Stange-Thomann,Kurt DeArellano,Robin Johnson,Lauren Linton,Paul A. McEwan,Kevin McKernan,Jessica A. Talamas,Andrea Tirrell,Andrea Tirrell,Wenjuan Ye,Wenjuan Ye,Andrew Zimmer,Robert D. Barber,Isaac K. O. Cann,David E. Graham,David A. Grahame,Adam M. Guss,Reiner Hedderich,Cheryl Ingram-Smith,Cheryl Ingram-Smith,Cheryl Ingram-Smith,H. Craig Kuettner,Joseph A. Krzycki,Joseph A. Krzycki,John A. Leigh,Weixi Li,Jinfeng Liu,Biswarup Mukhopadhyay,John N. Reeve,Kerry S. Smith,Timothy A. Springer,Timothy A. Springer,Timothy A. Springer,Lowell Umayam,Owen White,Robert H. White,Everly Conway de Macario,Everly Conway de Macario,James G. Ferry,Ken F. Jarrell,Ken F. Jarrell,Hua Jing,Hua Jing,Hua Jing,Alberto J.L. Macario,Ian T. Paulsen,Ian T. Paulsen,Ian T. Paulsen,Matthew A. Pritchett,Kevin R. Sowers,Ronald V. Swanson,Steven H. Zinder,Steven H. Zinder,Eric S. Lander,Eric S. Lander,Eric S. Lander,William W. Metcalf,Bruce W. Birren +76 more
TL;DR: The complete genome sequence of an acetate-utilizing methanogen, Methanosarcina acetivorans C2A, is reported, which indicates the likelihood of undiscovered natural energy sources for methanogenesis, whereas the presence of single-subunit carbon monoxide dehydrogenases raises the possibility of nonmethanogenic growth.
References
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Journal ArticleDOI
Whole-genome random sequencing and assembly of Haemophilus influenzae Rd.
Fleischmann Rd,Adams,Owen White,Rebecca A. Clayton,Ewen F. Kirkness,Anthony R. Kerlavage,Carol J. Bult,J F Tomb,Brian Dougherty,Merrick Jm +9 more
TL;DR: 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 of the genome from the bacterium Haemophilus influenzae Rd.
Journal ArticleDOI
Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi
Claire M. Fraser,Sherwood R. Casjens,Wai Mun Huang,Granger G. Sutton,Rebecca A. Clayton,Raju Lathigra,Owen White,Karen A. Ketchum,Robert J. Dodson,Erin Hickey,Michelle L. Gwinn,Brian Dougherty,J F Tomb,Robert D. Fleischmann,Delwood Richardson,Jeremy Peterson,Anthony R. Kerlavage,John Quackenbush,Steven L. Salzberg,Mark S. Hanson,René Van Vugt,Nanette Palmer,Mark Raymond Adams,Jeannine D. Gocayne,Janice Weidman,Teresa Utterback,Larry Watthey,Lisa McDonald,Patricia Artiach,Cheryl Bowman,Stacey Garland,Claire Fujii,Matthew D. Cotton,Kurt Horst,Kevin Roberts,Bonnie Hatch,Hamilton O. Smith,J. Craig Venter +37 more
TL;DR: 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, which suggest their limited metabolic capacities reflect convergent evolution by gene loss from more metabolically competent progenitors.
Journal ArticleDOI
Genomic mapping by fingerprinting random clones: A mathematical analysis
TL;DR: Simple formulas are derived showing how the progress of a physical mapping project is affected by the nature of the fingerprinting scheme, and the analytic considerations involved in selecting an appropriate fingerprinting schemes for a particular project are discussed.
Journal ArticleDOI
Sequencing Multimegabase-Template DNA with BigDye Terminator Chemistry
TL;DR: Using the recently introduced BigDye terminators, large-template DNA can be directly sequenced with custom primers on automated instruments without additional manipulations of template DNA, thereby bypassing tedious subcloning steps.
Journal ArticleDOI
Theoretical analysis of library screening using a N-dimensional pooling strategy
TL;DR: The combined screening of DNA families and YAC DNA pools would allow an integrated construction of both genetic and physical maps of the human genome, that will also reduce the optimal number of meioses needed for a 1 centimorgan linkage map.
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