1887

Chaper 1 : Sequencing Microbial Genomes

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Ebook: Choose a downloadable PDF or ePub file. Chapter is a downloadable PDF file. File must be downloaded within 48 hours of purchase

Buy this Chapter
Digital (?) $15.00

Preview this chapter:
Zoom in
Zoomout

Sequencing Microbial Genomes, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555818180/9781555811518_Chap01-1.gif /docserver/preview/fulltext/10.1128/9781555818180/9781555811518_Chap01-2.gif

Abstract:

This chapter gives an overview of the strategies developed to sequence entire microbial genomes, and discusses the advantages and disadvantages of various approaches. For total-genome shotgun sequencing, the genomic DNA is fragmented into random pieces and subcloned directly into pUC, Ml3, or other vectors that accept insert sizes of 1 to 5 kbp. Typically, 6 to 10 genome equivalents are sequenced to cover the DNA molecule completely by using standard primers that prime at the end of the cloning vector. The primer-walking strategy has been tried primarily in the context of the yeast sequencing project. The method requires an ordered library of clones, either an overlapping set of large clones (e.g., a cosmid library) or an ordered set of discrete subclones (e.g., two 6-base cutter restriction digest libraries from a cosmid). Regardless of the sequencing strategy chosen in a particular project, there are four general phases of the sequencing process. They are , , , and. Only one genome project, the effort at the University of Wisconsin, made substantial progress with radioactive sequencing before changing to automated-sequencing strategies. There are two different kinds of sequencing laboratories that produce genomic sequence: sequencing factories and smaller laboratories with an output of 2 to 5 Mbp of genomic sequence per year. With increasing levels of automation, the sequence production costs will be reduced, and in the future it may be possible to reach 10 cents per finished base pair.

Citation: Sensen C. 1999. Sequencing Microbial Genomes, p 1-9. In Charlebois R (ed), Organization of the Prokaryotic Genome. ASM Press, Washington, DC. doi: 10.1128/9781555818180.ch1

Key Concept Ranking

Shotgun Sequencing
0.6833029
Sequence Assembly
0.6243226
Sequence Alignment
0.59355885
Sequencing Methods
0.53675854
0.6833029
Highlighted Text: Show | Hide
Loading full text...

Full text loading...

References

/content/book/10.1128/9781555818180.chap1
1. Ansorge, W.,, B. Sproat,, J. Stegemann,, and C. Schwager. 1986. A non-radioactive automated method for DNA sequence determination. J. Biochem. Biophys. Methods 13:315323.
2. Baer, R.,, A. T. Bankier,, M. D. Biggin,, P. L. Deininger,, P. J. Farrell,, T. G. Gibson,, G. Hatfull,, G. S. Hudson,, S. C. Satchwell,, C. Sequin,, P. S. Tuffiiell,, and B. G. Barrell. 1984. DNA sequence and expression of the B95-8 Epstein-Barr virus genome. Nature 310:207211.
3. Blattner, F. R.,, G. PlunkettIII,, C. A. Bloch,, N. T. Perna,, V. Burland,, M. Riley,, J. Collado-Vides,, J. D. Glassner,, C. K. Rhode,, G. F. Mayhew,, J. Gregor,, N. W. Davis,, H. A. Kirkpatrick,, M. A. Goeden,, D. J. Rose,, B. Mau,, and Y. Shao. 1997. The complete genome sequence of Escherichia coli K-12. Science 277:14531474.
4. Bonfield, J. K.,, K. F. Smith,, and R. Staden. 1995. A new DNA sequence assembly program. Nucleic Acids Res. 23:49924999.
5. Burland, V.,, G. PlunkettIII,, D. L. Daniels,, and F. R. Blattner. 1993. DNA sequence and analysis of 136 kilobases of the Escherichia coli genome: organizational symmetry around the origin of replication. Genomics 16:551561.
6. Charlebois, R. L.,, T. Gaasterland,, M. A. Ragan,, W. F. Doolittle,, and C. W. Sensen. 1996. The Sulfolobus solfataricus P2 genome project. FEBS Lett. 389:8891.
7. Dolan, M.,, A. Ally,, M. S. Purzycki,, W. Gilbert,, and P. M. Gillevet. 1995. Large-scale genomic sequencing: optimization of genomic chemical sequencing reactions. BioTechniques 19: 264274.
8. Elliott, S. J.,, L. A. Wainwright,, T. K. McDaniel,, K. G. Jarvis,, Y. K. Deng,, L.-C. Lai,, B. P. McNamara,, M. S. Donnenberg,, and J. B. Kaper. 1998. The complete sequence of the locus of enterocyte effacement (LEE) from enteropathogenic Escherichia coli E2348/69. Mol. Microbiol 28:14.
9. Fleischmann, R. D.,, M. D. Adams,, O. White,, R. A. Clayton,, E. F. Kirkness,, A. R. Kerlavage,, C. J. Bult,, J.-F. Tomb,, B. A. Dougherty,, J. M. Merrick,, K. McKenny,, G. Sutton,, W. FitzHugh,, C. Fields,, J. D. Gocayne,, J. Scott,, R. Shirley,, L.-I. Liu,, A. Glodek,, J. M. Kelley,, J. F. Weidman,, C. A. Phillips,, T. Spriggs,, E. Hedblom,, M. D. Cotton,, T. R. Utterback,, M. C. Hanna,, D. T. Nguyen,, D. M. Saudek,, R. C. Brandon,, L. D. Fine,, J. L. Fritchman,, J. L. Fuhrmann,, N. S. M. Geoghagen,, C. L. Gnehm,, L. A. McDonald,, K. V. Small,, C. M. Fraser,, H. O. Smith,, and J. C. Venter. 1995. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269:496512.
10. Fräser, C. M.,, J. D. Gocayne,, O. White,, M. D. Adams,, R. A. Clayton,, R. D. Fleischmann,, C. J. Bult,, A. R. Kerlavage,, G. Sutton,, J. M. Kelley,, J. L. Fritchman,, J. F. Weidman,, K. V. Small,, M. Sandusky,, J. Fuhrmann,, D. Nguyen,, T. R. Utterback,, D. M. Saudek,, C. A. Phillips,, J. M. Merrick,, J.-F. Tomb,, B. A. Dougherty,, K. F. Bott,, P.-C. Hu,, T. S. Lucier,, S. N. Peterson,, H. O. Smith,, C. A. HutchisonIII,, and J. C. Venter. 1995. The minimal gene complement of Mycoplasma genitalium . Science 270:397403.
11. Gaasterland, T.,, and C. W. Sensen. 1996. Fully automated genome analysis that reflects user needs and preferences. A detailed introduction to the MAGPIE system architecture. Biochimie (Paris) 78:302310.
12. Glaser, V. 1997. TIGR Conference highlights crucial issues of speed and cost of genome sequencing. Genet. Eng. News 17:1.
13. Gordon, P., et al. Unpublished data.
14. Haas, S.,, M. Vingron,, A. Poustka,, and S. Wiemann. 1998. Primer design for large scale sequencing. Nucleic Acids Res. 26:30063012.
15. Koop, B. F.,, L. Rowan,, W.-Q. Chen,, P. Deshpande,, H. Lee,, and L. Hood. 1993. Sequence length and error analysis of Sequenase and automated Taq cycle sequencing methods. BioTechniques 14:442447.
16. Kunst, F.,, N. Ogasawara,, I. Moszer, A. M. Albertini,, G. Alloni,, V. Azevedo,, M. G. Bertero,, P. Bessières,, A. Bolotin,, S. Bordiert,, R. Borriss,, L. Boursier,, A. Brans,, M. Braun,, S. C. Brignell,, S. Bron,, S. Brouillet,, C. V. Bruschi,, B. Caldwell,, V. Capuano,, N. M. Carter,, S.-K. Choi,, J.-J. Codani,, I. F. Connerton,, N. J. Cummings,, R. A. Daniel,, F. Denizot,, K. M. Devine,, A. Düsterhöft,, S. D. Ehrlich,, P. T. Emmerson,, K. D. Entian,, J. Errington,, C. Fabret,, E. Ferrari,, D. Foulger,, C. Fritz,, M. Fujita,, Y. Fujita,, S. Fuma,, A. Galizzi,, N. Galleron,, S.-Y. Ghim,, P. Glaser,, A. Goffeau,, E. J. Golightly,, G. Grandi,, G. Giuseppi,, B. J. Guy,, K. Haga,, J. Haiech,, C. R. Harwood,, A. Henaut,, H. Hilbert,, S. Holsappel,, S. Hosono,, M.-F. Hullo,, M. Itaya,, L. Jones,, B. Joris,, D. Karamata,, Y. Kashahara,, M. Klaerr-Blanchard,, C. Klein,, Y. Kobayashi,, P. Koetter,, G. Koningstein,, S. Krogh,, M. Kumano,, K. Kurita,, A. Lapidus,, S. Lardinois,, J. Lauber,, V. LazareviC,., S.-M. Lee,, A. Levine,, H. Liu,, S. Masuda,, C. Mauël,, C. Médigue,, N. Medina,, R. P. Mellado,, M. Mizuno,, D. Moestl,, S. Nakai,, M. Noback,, D. Noone,, M. O'Reilly,, K. Ogawa,, A. Ogiwara,, B. Oudega,, S.-H. Park,, V. Parro,, T. M. Pohl,, D. Porteteile,, S. Porwollik,, A. M. Prescott,, E. Presecan,, P. PujiC,., B. Purnelle,, G. Rapoport,, M. Rey,, S. Reynolds,, M. Rieger,, C. Rivolta,, E. Rocha,, B. Roche,, M. Rose,, Y. Sadaie,, T. Sato,, E. Scanlan,, S. Schleich,, R. Schroeter,, F. Scoffone,, J. Sekiguchi,, A. Sekowska,, S. J. Seror,, P. Serror,, B.-S. Shin,, B. Soldo,, A. Sorokin,, E. Tacconi,, T. Takagi,, H. Takahashi,, K. Takemaru,, M. Takeuchi,, A. Tamakoshi,, T. Tanaka,, P. Terpstra,, A. Tognoni,, V. Tosato,, S. Uchiyama,, M. Vandenbol,, F. Vannier,, A. Vassarotti,, A. Viari,, R. Wambutt,, E. Wedler,, H. Wedler,, T. Weitzenegger,, P. Winters,, A. Wipat,, H. Yamamoto,, K. Yamane,, K. Yasumoto,, K. Yata,, K. Yoshida,, H.-F. Yoshikawa,, E. Zumstein,, H. Yoshikawa,, and A. Danchin. 1997. The complete genome sequence of the Gram-positive bacterium Bacillus subtilis . Nature 390:249256.
17. Lee, L. G.,, C. R. Cornell,, S. L. Woo,, R. D. Cheng,, B. F. McArdle,, C. W. Fuller,, N. D. Halloran,, and R. K. Wilson. 1992. DNA sequencing with dye-labelled terminators and T7 polymerase: effect of dyes and dNTPs on the incorporation of dye-terminators and probability analysis of termination fragments. Nucleic Acids Res. 20:24712483.
18. Panussis, D. A.,, M. W. Cook,, L. L. Rifkin,, J. E. Snider,, J. T. Strong,, R. M. McGrane,, R. K. Wilson,, and E. R. Mardis. 1998. A pneumatic device for rapid loading of DNA sequencing gels. Genome Res. 8:543548.
19. Sensen, C. W.,, H. P. Klenk,, R. K. Singh,, G. Allard,, C. C.-Y. Chan,, Q. Liu,, S. Penny,, F. Young,, M. Schenk,, T. Gaasterland,, W. F. Doolittle,, M. A. Ragan,, and R. L. Charlebois. 1996. Organizational characteristics and information content of an archaeal genome: 156 kbp of contiguous sequence from Sulfolobus solfataricus P2. Mol. Microbiol 22:175191.
20. Smith, L. M.,, J. Z. Sanders,, R. J. Kaiser,, P. Hughes,, C. Dodd,, C. R. Connel,, C. Heiner,, S. B. H. Kent,, and L. E. Hood. 1986. Fluorescence detection in automated DNA sequence analysis. Nature 321:674679.
21. Studier, F. 1989. A strategy for high-volume sequencing of cosmid DNAs: random and directed priming with a library of oligonucleotides. Proc. Natl. Acad. Sci. USA 86:69176921.
22. Venter, J. C.,, H. O. Smith,, and L. Hood. 1996. A new strategy for genome sequencing. Nature 381:364366.
23. Voss, H.,, S. Wiemann,, U. Wirkner,, C. Schwager,, J. Zimmermann,, J. Stegemann,, H. Erfle,, N. A. Hewitt,, T. Rupp,, and W. Ansorge. 1992. Automated DNA sequencing system resolving 1000 bases with fluorescein*-15-dATP as internal label. Methods Mol. Cell. Biol 3:153155.
24. Voss, H.,, S. Wiemann,, D. Grothues,, C. Sensen,, J. Zimmermann,, C. Schwager,, J. Stegemann,, H. Erfle,, T. Rupp,, and W. Ansorge. 1993. Automated low-redundancy large-scale DNA sequencing by primer walking. BioTechniques 15:714721.
25. Watson, J. D. 1990. The human genome project. Science 248:4449.
26. Wiemann, S.,, H. Voss,, C. Schwager,, T. Rupp,, J. Stegemann,, J. Zimmermann,, D. Grothues,, C. Sensen,, H. Erfle,, A. Banrevi,, and W. Ansorge. 1993. Sequencing and analysis of 51.6 kilobases on the left arm of chromosome XI from Saccharomyces cerevisiae reveals 23 open reading frames including the fas1 gene. Yeast 9: 13431348.

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error