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Method: Genome-wide detection of chromosomal rearrangements, indels, and mutations in circular chromosomes by short read sequencing
- Ole Skovgaard,
- Mads Bak,
- Anders Løbner-Olesen,
- and Niels Tommerup
Genome Res. August 2011 21: 1388-1393; Published in Advance May 9, 2011, doi:10.1101/gr.117416.110
...tandem repeats, and major genomic rearrangements. The chromosomal rearrangements identified in this study were only detected because we used DNA template isolated from a fast-growing bacterial culture and combined sequence determination and copy number variation analysis. These rearrangements would...
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Method: Strand-specific deep sequencing of the transcriptome
- Ana P. Vivancos,
- Marc Güell,
- Juliane C. Dohm,
- Luis Serrano,
- and Heinz Himmelbauer
Genome Res. July 2010 20: 989-999; Published in Advance June 2, 2010, doi:10.1101/gr.094318.109
...and subjected to SYBR green real-time PCR. Non-reversetranscribed controls were included for each gene, as well as a genomic DNA dilution series. DSSS signal corresponds to the log2 transformed mean number of counts along the gene. Strand-specific transcriptome sequencing Genome Research 991 www..org Pearson...
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RESEARCH: Multiplex Sequencing of 1.5 Mb of the Mycobacterium leprae Genome
- Douglas R. Smith,
- Peter Richterich,
- Marc Rubenfield,
- Philip W. Rice,
- Carol Butler,
- Hong-Mei Lee,
- Susan Kirst,
- Kristin Gundersen,
- Kari Abendschan,
- Qinxue Xu,
- Maria Chung,
- Craig Deloughery,
- Tyler Aldredge,
- James Maher,
- Ronald Lundstrom,
- Craig Tulig,
- Kathleen Falls,
- Joan Imrich,
- Dana Torrey,
- Marcy Engelstein,
- Gary Breton,
- Deepika Madan,
- Raymond Nietupski,
- Bruce Seitz,
- Steven Connelly,
- Steven McDougall,
- Hershel Safer,
- Rene Gibson,
- Lynn Doucette-Stamm,
- Karin Eiglmeier,
- Staffan Bergh,
- Stewart T. Cole,
- Keith Robison,
- Laura Richterich,
- Jason Johnson,
- George M. Church,
- and Jen-i Mao
Genome Res. August 1, 1997 7: 802-819; doi:10.1101/gr.7.8.802
....5 Mb of genomic DNA from Mycobacterium leprae was determined using computer-assisted multiplex sequencing technology. This brings the 2.8-Mb M. leprae genome sequence to ∼66% completion. The sequences, derived from 43 recombinant cosmids, contain 1046 putative protein-coding genes, 44 repetitive...
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ARTICLE: A Complete Sequence of the T. tengcongensis Genome
- Qiyu Bao,
- Yuqing Tian,
- Wei Li,
- Zuyuan Xu,
- Zhenyu Xuan,
- Songnian Hu,
- Wei Dong,
- Jian Yang,
- Yanjiong Chen,
- Yanfen Xue,
- Yi Xu,
- Xiaoqin Lai,
- Li Huang,
- Xiuzhu Dong,
- Yanhe Ma,
- Lunjiang Ling,
- Huarong Tan,
- Runsheng Chen,
- Jian Wang,
- Jun Yu,
- and Huanming Yang
Genome Res. May 1, 2002 12: 689-700; doi:10.1101/gr.219302
...of the interesting features of the T. tengcongensis genome is that 86.7% of its genes are encoded on the leading strand of DNA replication. Based on protein sequence similarity, the T. tengcongensis genome is most similar to that of Bacillus halodurans , a mesophilic eubacterium, among all fully sequenced...
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ARTICLE: Genome sequence of Blochmannia pennsylvanicus indicates parallel evolutionary trends among bacterial mutualists of insects
- Patrick H. Degnan,
- Adam B. Lazarus,
- and Jennifer J. Wernegreen
Genome Res. August 2005 15: 1023-1033; doi:10.1101/gr.3771305
...the implications of variability on the physiology and ecology of both symbiotic partners, and to clarify the levels and timing of selection that shape this long-term bacterium–ant association. Methods Blochmannia sequencing and assembly B. pennsylvanicus genomic DNA (gDNA) was prepared from worker and larvae C...
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Letter: Complete genome of the cellulolytic thermophile Acidothermus cellulolyticus 11B provides insights into its ecophysiological and evolutionary adaptations
- Ravi D. Barabote,
- Gary Xie,
- David H. Leu,
- Philippe Normand,
- Anamaria Necsulea,
- Vincent Daubin,
- Claudine Médigue,
- William S. Adney,
- Xin Clare Xu,
- Alla Lapidus,
- Rebecca E. Parales,
- Chris Detter,
- Petar Pujic,
- David Bruce,
- Celine Lavire,
- Jean F. Challacombe,
- Thomas S. Brettin,
- and Alison M. Berry
Genome Res. June 2009 19: 1033-1043; Published in Advance March 6, 2009, doi:10.1101/gr.084848.108
...Record: NC_ 008578) was sequenced and annotated by the Joint Genome Institute, U.S. Department of Energy. Large (40 kb), medium (8 kb), and small (3 kb) insert DNA libraries were sequenced using the random shotgun method with an average success rate of 96% and average high-quality read lengths of 685...
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ARTICLE: Tropheryma whipplei Twist: A Human Pathogenic Actinobacteria With a Reduced Genome
- Didier Raoult,
- Hiroyuki Ogata,
- Stéphane Audic,
- Catherine Robert,
- Karsten Suhre,
- Michel Drancourt,
- and Jean-Michel Claverie
Genome Res. August 2003 13: 1800-1809; doi:10.1101/gr.1474603
...disclosed &lt;10-4 HEL cell DNA contamination. Plasmid clones were sequenced at both ends of the insert with flanking vector sequences as primers. Dye primer reactions were analyzed on an L1-COR 4200L, and six genomic equivalents were sequenced. We generated a second library B by cloning 20-kb fragments...
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LETTER: Genome sequence of a proteolytic (Group I) Clostridium botulinum strain Hall A and comparative analysis of the clostridial genomes
- Mohammed Sebaihia,
- Michael W. Peck,
- Nigel P. Minton,
- Nicholas R. Thomson,
- Matthew T.G. Holden,
- Wilfrid J. Mitchell,
- Andrew T. Carter,
- Stephen D. Bentley,
- David R. Mason,
- Lisa Crossman,
- Catherine J. Paul,
- Alasdair Ivens,
- Marjon H.J. Wells-Bennik,
- Ian J. Davis,
- Ana M. Cerdeño-Tárraga,
- Carol Churcher,
- Michael A. Quail,
- Tracey Chillingworth,
- Theresa Feltwell,
- Audrey Fraser,
- Ian Goodhead,
- Zahra Hance,
- Kay Jagels,
- Natasha Larke,
- Mark Maddison,
- Sharon Moule,
- Karen Mungall,
- Halina Norbertczak,
- Ester Rabbinowitsch,
- Mandy Sanders,
- Mark Simmonds,
- Brian White,
- Sally Whithead,
- and Julian Parkhill
Genome Res. July 2007 17: 1082-1092; Published in Advance May 22, 2007, doi:10.1101/gr.6282807
...DNA, indicating a stable genomic content, in strong contrast to the fluid genome of Clostridium difficile , which can form longer-term relationships with its host. Overall, the genome indicates that C. botulinum is adapted to a saprophytic lifestyle both in soil and aquatic environments...
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LETTER: Comparative Analysis of Chloroplast Genomes: Functional Annotation, Genome-Based Phylogeny, and Deduced Evolutionary Patterns
- Javier De Las Rivas,
- Juan Jose Lozano,
- and Angel R. Ortiz
Genome Res. April 1, 2002 12: 567-583; doi:10.1101/gr.209402
...of using PSI-BLAST . Then, a comparative genomics study is carried out using techniques borrowed from multivariate analysis. RESULTS AND DISCUSSION Functional Annotations of cpDNA Proteins Quality of Annotations All protein sequences from 19 complete chloroplast s (cpDNA) were compared against the 3168...
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REVIEW: A P1-based physical map of the Drosophila euchromatic genome.
- W Kimmerly,
- K Stultz,
- S Lewis,
- K Lewis,
- V Lustre,
- R Romero,
- J Benke,
- D Sun,
- G Shirley,
- C Martin,
- and M Palazzolo
Genome Res. May 1996 6: 414-430; doi:10.1101/gr.6.5.414
.... Taylor, R.G., , Walker, D.C. , McInnes. R.R. Taylor, R.G., Walker, D.C. and McInnes. R.R. 1993 . E. coli host strains significantly affect the quality of small scale plasmid DNA preparations used for sequencing. Nucleic Acids Res. 21 : 1677 – 1678 . Wakimoto, B.T., , Turner, F.R. , Kaufman. T.C. Wakimoto...

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