Whole genome shotgun sequencing guided-by bioinformatics pipelines - An optimized approach for an established technique

Kaiser O, Bartels D, Bekel T, Goesmann A, Kespohl S, Pühler A, Meyer F (2003)
JOURNAL OF BIOTECHNOLOGY 106(2-3): 121-133.

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Zeitschriftenaufsatz | Veröffentlicht | Englisch
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Abstract / Bemerkung
While the sequencing of bacterial genomes has become a routine procedure at major sequencing centers, there are still a number of genome projects at small- or medium-size facilities. For these facilities a maximum of control over sequencing, assembling and finishing is essential. At the same time, facilities have to be able to co-operate at minimum costs for the overall project. We have established a pipeline for the distributed sequencing of Alcanivorax borkumensis SK2, Azoarcus sp. BH72, Clavibacter michiganensis subsp. michiganensis NCPPB382, Sorangium cellulosum So ce56 and Xanthomonas campestris pv. vesicatoria 85-10. Our pipeline relies on standard tools (e.g. PHRED/PHRAP, CAP3 and Consed/Autofinish) wherever possible, supplementing them with new tools (BioMake and BACCardI) to achieve the aims described above. (C) 2003 Elsevier B.V. All rights reserved.
Erscheinungsjahr
Zeitschriftentitel
JOURNAL OF BIOTECHNOLOGY
Band
106
Ausgabe
2-3
Seite(n)
121-133
ISSN
PUB-ID

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Kaiser O, Bartels D, Bekel T, et al. Whole genome shotgun sequencing guided-by bioinformatics pipelines - An optimized approach for an established technique. JOURNAL OF BIOTECHNOLOGY. 2003;106(2-3):121-133.
Kaiser, O., Bartels, D., Bekel, T., Goesmann, A., Kespohl, S., Pühler, A., & Meyer, F. (2003). Whole genome shotgun sequencing guided-by bioinformatics pipelines - An optimized approach for an established technique. JOURNAL OF BIOTECHNOLOGY, 106(2-3), 121-133. doi:10.1016/j.jbiotec.2003.08.008
Kaiser, O., Bartels, D., Bekel, T., Goesmann, A., Kespohl, S., Pühler, A., and Meyer, F. (2003). Whole genome shotgun sequencing guided-by bioinformatics pipelines - An optimized approach for an established technique. JOURNAL OF BIOTECHNOLOGY 106, 121-133.
Kaiser, O., et al., 2003. Whole genome shotgun sequencing guided-by bioinformatics pipelines - An optimized approach for an established technique. JOURNAL OF BIOTECHNOLOGY, 106(2-3), p 121-133.
O. Kaiser, et al., “Whole genome shotgun sequencing guided-by bioinformatics pipelines - An optimized approach for an established technique”, JOURNAL OF BIOTECHNOLOGY, vol. 106, 2003, pp. 121-133.
Kaiser, O., Bartels, D., Bekel, T., Goesmann, A., Kespohl, S., Pühler, A., Meyer, F.: Whole genome shotgun sequencing guided-by bioinformatics pipelines - An optimized approach for an established technique. JOURNAL OF BIOTECHNOLOGY. 106, 121-133 (2003).
Kaiser, O., Bartels, D., Bekel, Thomas, Goesmann, Alexander, Kespohl, S., Pühler, Alfred, and Meyer, F. “Whole genome shotgun sequencing guided-by bioinformatics pipelines - An optimized approach for an established technique”. JOURNAL OF BIOTECHNOLOGY 106.2-3 (2003): 121-133.

14 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

Whole-genome sequencing and gene mapping of a newly isolated lytic enterococcal bacteriophage EFRM31.
Fard RM, Barton MD, Arthur JL, Heuzenroeder MW., Arch Virol 155(11), 2010
PMID: 20844906
The Sequence Analysis and Management System -- SAMS-2.0: data management and sequence analysis adapted to changing requirements from traditional sanger sequencing to ultrafast sequencing technologies.
Bekel T, Henckel K, Küster H, Meyer F, Mittard Runte V, Neuweger H, Paarmann D, Rupp O, Zakrzewski M, Pühler A, Stoye J, Goesmann A., J Biotechnol 140(1-2), 2009
PMID: 19297685
The genome sequence of the tomato-pathogenic actinomycete Clavibacter michiganensis subsp. michiganensis NCPPB382 reveals a large island involved in pathogenicity.
Gartemann KH, Abt B, Bekel T, Burger A, Engemann J, Flügel M, Gaigalat L, Goesmann A, Gräfen I, Kalinowski J, Kaup O, Kirchner O, Krause L, Linke B, McHardy A, Meyer F, Pohle S, Rückert C, Schneiker S, Zellermann EM, Pühler A, Eichenlaub R, Kaiser O, Bartels D., J Bacteriol 190(6), 2008
PMID: 18192381
The genome of Xanthomonas campestris pv. campestris B100 and its use for the reconstruction of metabolic pathways involved in xanthan biosynthesis.
Vorhölter FJ, Schneiker S, Goesmann A, Krause L, Bekel T, Kaiser O, Linke B, Patschkowski T, Rückert C, Schmid J, Sidhu VK, Sieber V, Tauch A, Watt SA, Weisshaar B, Becker A, Niehaus K, Pühler A., J Biotechnol 134(1-2), 2008
PMID: 18304669
Complete genome sequence of the myxobacterium Sorangium cellulosum.
Schneiker S, Perlova O, Kaiser O, Gerth K, Alici A, Altmeyer MO, Bartels D, Bekel T, Beyer S, Bode E, Bode HB, Bolten CJ, Choudhuri JV, Doss S, Elnakady YA, Frank B, Gaigalat L, Goesmann A, Groeger C, Gross F, Jelsbak L, Jelsbak L, Kalinowski J, Kegler C, Knauber T, Konietzny S, Kopp M, Krause L, Krug D, Linke B, Mahmud T, Martinez-Arias R, McHardy AC, Merai M, Meyer F, Mormann S, Muñoz-Dorado J, Perez J, Pradella S, Rachid S, Raddatz G, Rosenau F, Rückert C, Sasse F, Scharfe M, Schuster SC, Suen G, Treuner-Lange A, Velicer GJ, Vorhölter FJ, Weissman KJ, Welch RD, Wenzel SC, Whitworth DE, Wilhelm S, Wittmann C, Blöcker H, Pühler A, Müller R., Nat Biotechnol 25(11), 2007
PMID: 17965706
Genome sequence of the ubiquitous hydrocarbon-degrading marine bacterium Alcanivorax borkumensis.
Schneiker S, Martins dos Santos VA, Bartels D, Bekel T, Brecht M, Buhrmester J, Chernikova TN, Denaro R, Ferrer M, Gertler C, Goesmann A, Golyshina OV, Kaminski F, Khachane AN, Lang S, Linke B, McHardy AC, Meyer F, Nechitaylo T, Pühler A, Regenhardt D, Rupp O, Sabirova JS, Selbitschka W, Yakimov MM, Timmis KN, Vorhölter FJ, Weidner S, Kaiser O, Golyshin PN., Nat Biotechnol 24(8), 2006
PMID: 16878126
The crystal structure of hypothetical methyltransferase from Thermus thermophilus HB8.
Sasaki C, Sugiura I, Ebihara A, Tamura T, Sugio S, Inagaki K., Proteins 64(2), 2006
PMID: 16700050
Complete genome of the mutualistic, N2-fixing grass endophyte Azoarcus sp. strain BH72.
Krause A, Ramakumar A, Bartels D, Battistoni F, Bekel T, Boch J, Böhm M, Friedrich F, Hurek T, Krause L, Linke B, McHardy AC, Sarkar A, Schneiker S, Syed AA, Thauer R, Vorhölter FJ, Weidner S, Pühler A, Reinhold-Hurek B, Kaiser O, Goesmann A., Nat Biotechnol 24(11), 2006
PMID: 17057704
BACCardI--a tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison.
Bartels D, Kespohl S, Albaum S, Drüke T, Goesmann A, Herold J, Kaiser O, Pühler A, Pfeiffer F, Raddatz G, Stoye J, Meyer F, Schuster SC., Bioinformatics 21(7), 2005
PMID: 15514001
Complete genome sequence and analysis of the multiresistant nosocomial pathogen Corynebacterium jeikeium K411, a lipid-requiring bacterium of the human skin flora.
Tauch A, Kaiser O, Hain T, Goesmann A, Weisshaar B, Albersmeier A, Bekel T, Bischoff N, Brune I, Chakraborty T, Kalinowski J, Meyer F, Rupp O, Schneiker S, Viehoever P, Pühler A., J Bacteriol 187(13), 2005
PMID: 15968079
Shotgun sequencing of the negative-sense RNA genome of the rhabdovirus Maize mosaic virus.
Reed SE, Tsai CW, Willie KJ, Redinbaugh MG, Hogenhout SA., J Virol Methods 129(1), 2005
PMID: 16005085
Insights into genome plasticity and pathogenicity of the plant pathogenic bacterium Xanthomonas campestris pv. vesicatoria revealed by the complete genome sequence.
Thieme F, Koebnik R, Bekel T, Berger C, Boch J, Büttner D, Caldana C, Gaigalat L, Goesmann A, Kay S, Kirchner O, Lanz C, Linke B, McHardy AC, Meyer F, Mittenhuber G, Nies DH, Niesbach-Klösgen U, Patschkowski T, Rückert C, Rupp O, Schneiker S, Schuster SC, Vorhölter FJ, Weber E, Pühler A, Bonas U, Bartels D, Kaiser O., J Bacteriol 187(21), 2005
PMID: 16237009

43 References

Daten bereitgestellt von Europe PubMed Central.

Basic local alignment search tool.
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ., J. Mol. Biol. 215(3), 1990
PMID: 2231712

AUTHOR UNKNOWN, 0
ARACHNE: a whole-genome shotgun assembler.
Batzoglou S, Jaffe DB, Stanley K, Butler J, Gnerre S, Mauceli E, Berger B, Mesirov JP, Lander ES., Genome Res. 12(1), 2002
PMID: 11779843
On the high value of low standards.
Branscomb E, Predki P., J. Bacteriol. 184(23), 2002
PMID: 12426325
Clavibacter: a new genus containing some phythopathogenic coryneform bacteria, including Clavibacter xyli supsp. xyli sp. nov., subsp. nov. and Clavibacter xyli supsp. cynodontis subsp. nov., pathogens that cause ratoon stunting disease of sugarcane and bermudagrass stunting disease
Davis, Int. J. Syst. Bacteriol. 34(), 1984
Automated DNA sequencing of the human HPRT locus.
Edwards A, Voss H, Rice P, Civitello A, Stegemann J, Schwager C, Zimmermann J, Erfle H, Caskey CT, Ansorge W., Genomics 6(4), 1990
PMID: 2341149
Base-calling of automated sequencer traces using phred. I. Accuracy assessment.
Ewing B, Hillier L, Wendl MC, Green P., Genome Res. 8(3), 1998
PMID: 9521921
Whole-genome random sequencing and assembly of Haemophilus influenzae Rd.
Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, Kerlavage AR, Bult CJ, Tomb JF, Dougherty BA, Merrick JM., Science 269(5223), 1995
PMID: 7542800
Cloning and assembly strategies in microbial genome projects.
Frangeul L, Nelson KE, Buchrieser C, Danchin A, Glaser P, Kunst F., Microbiology (Reading, Engl.) 145 ( Pt 10)(), 1999
PMID: 10537184
The value of complete microbial genome sequencing (you get what you pay for).
Fraser CM, Eisen JA, Nelson KE, Paulsen IT, Salzberg SL., J. Bacteriol. 184(23), 2002
PMID: 12426324

AUTHOR UNKNOWN, 0
Life with 6000 genes.
Goffeau A, Barrell BG, Bussey H, Davis RW, Dujon B, Feldmann H, Galibert F, Hoheisel JD, Jacq C, Johnston M, Louis EJ, Mewes HW, Murakami Y, Philippsen P, Tettelin H, Oliver SG., Science 274(5287), 1996
PMID: 8849441
Consed: a graphical tool for sequence finishing.
Gordon D, Abajian C, Green P., Genome Res. 8(3), 1998
PMID: 9521923
Automated finishing with autofinish.
Gordon D, Desmarais C, Green P., Genome Res. 11(4), 2001
PMID: 11282977
Whole-genome disassembly.
Green P., Proc. Natl. Acad. Sci. U.S.A. 99(7), 2002
PMID: 11904394
Plasmid transformation of Escherichia coli and other bacteria.
Hanahan D, Jessee J, Bloom FR., Meth. Enzymol. 204(), 1991
PMID: 1943786
CAP3: A DNA sequence assembly program.
Huang X, Madan A., Genome Res. 9(9), 1999
PMID: 10508846
Azoarcus sp. strain BH72 as a model for nitrogen-fixing grass endophytes.
Hurek T, Reinhold-Hurek B., J. Biotechnol. 106(2-3), 2003
PMID: 14651859
Whole-genome sequence assembly for mammalian genomes: Arachne 2.
Jaffe DB, Butler J, Gnerre S, Mauceli E, Lindblad-Toh K, Mesirov JP, Zody MC, Lander ES., Genome Res. 13(1), 2003
PMID: 12529310
The complete Corynebacterium glutamicum ATCC 13032 genome sequence and its impact on the production of L-aspartate-derived amino acids and vitamins.
Kalinowski J, Bathe B, Bartels D, Bischoff N, Bott M, Burkovski A, Dusch N, Eggeling L, Eikmanns BJ, Gaigalat L, Goesmann A, Hartmann M, Huthmacher K, Kramer R, Linke B, McHardy AC, Meyer F, Mockel B, Pfefferle W, Puhler A, Rey DA, Ruckert C, Rupp O, Sahm H, Wendisch VF, Wiegrabe I, Tauch A., J. Biotechnol. 104(1-3), 2003
PMID: 12948626

AUTHOR UNKNOWN, 0
Genomic mapping by fingerprinting random clones: a mathematical analysis.
Lander ES, Waterman MS., Genomics 2(3), 1988
PMID: 3294162
GenDB--an open source genome annotation system for prokaryote genomes.
Meyer F, Goesmann A, McHardy AC, Bartels D, Bekel T, Clausen J, Kalinowski J, Linke B, Rupp O, Giegerich R, Puhler A., Nucleic Acids Res. 31(8), 2003
PMID: 12682369
YACs, BACs, PACs and MACs: artificial chromosomes as research tools.
Monaco AP, Larin Z., Trends Biotechnol. 12(7), 1994
PMID: 7765076
The phusion assembler.
Mullikin JC, Ning Z., Genome Res. 13(1), 2003
PMID: 12529309
Whole-genome DNA sequencing
Myers, Comput. Sci. Eng. 1(), 1999
Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima.
Nelson KE, Clayton RA, Gill SR, Gwinn ML, Dodson RJ, Haft DH, Hickey EK, Peterson JD, Nelson WC, Ketchum KA, McDonald L, Utterback TR, Malek JA, Linher KD, Garrett MM, Stewart AM, Cotton MD, Pratt MS, Phillips CA, Richardson D, Heidelberg J, Sutton GG, Fleischmann RD, Eisen JA, White O, Salzberg SL, Smith HO, Venter JC, Fraser CM., Nature 399(6734), 1999
PMID: 10360571
Characterisation, genome size and genetic manipulation of the myxobacterium Sorangium cellulosum So ce56.
Pradella S, Hans A, Sproer C, Reichenbach H, Gerth K, Beyer S., Arch. Microbiol. 178(6), 2002
PMID: 12420170
Azoarcus gen. nov., nitrogen-fixing proteobacteria associated with roots of Kallar grass (Leptochloafusca (L.) Kunth) and description of two species Azoarcus indigens sp. nov. and Azoarcus communis sp. nov.
Reinhold-Hurek, Int. J. Syst. Bacteriol. 43(), 1993
Close association of azospirillum and diazotrophic rods with different root zones of kallar grass.
Reinhold B, Hurek T, Niemann EG, Fendrik I., Appl. Environ. Microbiol. 52(3), 1986
PMID: 16347149
Gaps in the Human Genome Project.
Roach JC, Siegel AF, van den Engh G, Trask B, Hood L., Nature 401(6756), 1999
PMID: 10553897
DNA sequencing with chain-terminating inhibitors.
Sanger F, Nicklen S, Coulson AR., Proc. Natl. Acad. Sci. U.S.A. 74(12), 1977
PMID: 271968
Cloning and stable maintenance of 300-kilobase-pair fragments of human DNA in Escherichia coli using an F-factor-based vector.
Shizuya H, Birren B, Kim UJ, Mancino V, Slepak T, Tachiiri Y, Simon M., Proc. Natl. Acad. Sci. U.S.A. 89(18), 1992
PMID: 1528894
Modeling the feasibility of whole genome shotgun sequencing using a pairwise end strategy.
Siegel AF, van den Engh G, Hood L, Trask B, Roach JC., Genomics 68(3), 2000
PMID: 10995565
Strategy to sequence the genome of Corynebacterium glutamicum ATCC 13032: use of a cosmid and a bacterial artificial chromosome library.
Tauch A, Homann I, Mormann S, Ruberg S, Billault A, Bathe B, Brand S, Brockmann-Gretza O, Ruckert C, Schischka N, Wrenger C, Hoheisel J, Mockel B, Huthmacher K, Pfefferle W, Puhler A, Kalinowski J., J. Biotechnol. 95(1), 2002
PMID: 11879709

AUTHOR UNKNOWN, 0
Complete nucleotide sequence of two generations of a bacterial artificial chromosome cloning vector.
Wang K, Boysen C, Shizuya H, Simon MI, Hood L., BioTechniques 23(6), 1997
PMID: 9421622
The complete sequence of the 1,683-kb pSymB megaplasmid from the N2-fixing endosymbiont Sinorhizobium meliloti.
Finan TM, Weidner S, Wong K, Buhrmester J, Chain P, Vorholter FJ, Hernandez-Lucas I, Becker A, Cowie A, Gouzy J, Golding B, Puhler A., Proc. Natl. Acad. Sci. U.S.A. 98(17), 2001
PMID: 11481431
Alcanivorax borkumensis gen. nov., sp. nov., a new, hydrocarbon-degrading and surfactant-producing marine bacterium.
Yakimov MM, Golyshin PN, Lang S, Moore ER, Abraham WR, Lunsdorf H, Timmis KN., Int. J. Syst. Bacteriol. 48 Pt 2(), 1998
PMID: 9731272

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