PCR-assisted contig extension: Stepwise strategy for bacterial genome closure

BioTechniques

Volumn 34, Issue 3, 2003, Pages 626-632

  Carraro, D M ^a   Camargo, A A ^a   Salim, A C M ^a   Grivet, M ^b   Vasconcelos, A T ^c   Simpson, A J G ^a,d  

^a LUDWIG INSTITUTE FOR CANCER RESEARCH   (Brazil)

^b PONTIFICAL CATHOLIC UNIVERSITY OF RIO DE JANEIRO   (Brazil)

^c LABORATÓRIO NACIONAL DE COMPUTAÇÃO CIENTÍFICA   (Brazil)

^d LUDWIG INSTITUTE FOR CANCER RESEARCH   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA; DNA; RNA;

CONTIG EXTENSION;

GENETIC ENGINEERING;

BACTERIAL DNA; RNA 16S; RNA 5S;

ARTICLE; BACTERIAL GENOME; CHROMOBACTERIUM; COST; DNA SEQUENCE; NONHUMAN; OPERON; POLYMERASE CHAIN REACTION; RNA GENE;

BACTERIA (MICROORGANISMS); CHROMOBACTERIUM; PROKARYOTA;

EID: 0037336262     PISSN: 07366205     EISSN: None     Source Type: Journal    
DOI: 10.2144/03343dd05     Document Type: Article

References (17)

1. Tettelin, H., D. Radune, S. Kasif, H. Khouri, and S.L. Salzberg. 1999. Optimized multiplex PCR: efficiently closing a whole-genome shotgun sequencing project. Genomics 15:500-507.
2. Frohme, M., A.A. Camargo, C. Czink, A.Y. Matsukuma, A.J.G. Simpson, D. Hoheisel, and S. Verjovski-Almeida. 2001. Direct gap closure in large-scale sequencing project. Genome Res. 11:901-903.
3. Heiner, C.R., K.L. Hunkapiller, S.M. Chen, J.I. Glass, and E.Y. Chen. 1998. Sequencing multimegabase-template DNA with BigDye terminator chemistry. Genome Res. 8:557-561.
4. Krin, E., F. Hommais, O. Soutourina, S. Ngo, A. Danchin, and P. Bertin. 2001. Description and application of a rapid method for genomic DNA direct sequencing. FEMS Microbiol. Lett. 30:229-233.
5. Weinel, C., B. Tummler, H. Hilbert, K.E. Nelson, and C. Kiewitz. 2001. General method of rapid Smith/Birnstiel mapping adds for gap closure in shotgun microbial genome sequencing projects: application to Pseudomonas putida KT2440. Nucleic Acids Res. 29:E110.
6. Couch, F.J., J.M. Rommens, S.L. Neuhausen, C. Belanger, M. Dumont, K. Abel, R. Bell, S. Berry, et al. 1996. Generation of an integrated transcription map of the BRCA2 region on chromosome 13q12-q13. Genomics 36:86-99.
7. Hui, E.K., P.C. Wang, and S.J. Lo. 1995. Strategies for cloning unknown cellular flanking DNA sequences from foreign integrants. Cell Mol. Life Sci. 54:1403-1411.
8. Liu, Y.G. and R.F. Whittier. 1995. Thermal asymmetric interlaced PCR: automatable amplification and sequencing of insert end fragments from P1 and YAC clones for chromosome walking. Genomics 25:674-681.
9. Mishra, R.N., S.L. Singla-Pareek, S. Nair, S.K. Sopory, and M.K. Reddy. 2002. Directional genome walking using PCR. BioTechniques 33:831-834.
10. Spertini, D., C. Beliveau, and G. Bellemare. 1999. Screening of transgenic plants by amplification of unknown genomic DNA flanking T-DNA. BioTechniques 27:308-314.
11. Swensen, J. 1996. PCR with random primers to obtain sequence from yeast artificial chromosome insert ends or plasmids. BioTechniques 20:486-491.
12. Swensen, J., M. Hoffman, M.H. Skolnick, and S.L. Neuhausen. 1997. Identification of a 14Kb deletion involving the promoter region of BRCA1 in breast cancer family. Hum. Mol. Genet. 6:1513-1517.
13. Zhou, Y.X., R.J. Newton, and J.H. Gould. 1997. A simple method for identifying plant/T-DNA junction sequences resulting from Agrobacterium-mediated DNA transformation. Plant Mol. Biol. Rep. 15:246-254.
14. Gordon, D., C. Abajian, and P. Green. 1998. Consed: a graphical tool for sequence finishing. Genome Res. 8:195-202.
15. Lukacsovich, T. and D. Yamamoto. 2001. Trap a gene and find out its function: toward functional genomics in Drosophila. J. Neurogenet. 15:147-168.
16. Mills, D.A. 2001. Mutagenesis in the post genomics era: tools for generating insertional mutations in the lactic acid bacteria. Curr. Opin. Biotechnol. 12:503-509.
17. Zheng, S.J., B. Henken, E. Sofiari, E. Jacobsen, F.A. Krens, and C. Kik. 2001. Molecular characterization of transgenic shallots (Allium cepa L.) by adaptor ligation PCR (AL-PCR) and sequencing of genomic DNA flanking T-DNA borders. Transgenic Res. 10:237-245.