Abstract
The pyrosequencing methodology was applied in 2005 by 454 Lifesciences to the emerging field of next generation sequencing (NGS), revolutionizing the way of DNA sequencing. In the last years the same strategy grew up and was technologically updated, reaching a high throughput in terms of amount of generated sequences (reads) per run and in terms of length of sequence up to values of 800–1,000 bases. These features of pyrosequencing perfectly fit to bacterial genome sequencing for the de novo assemblies and resequencing as well. The approaches of shotgun and paired ends sequencing allow the bacterial genome finishing providing a high-quality data in few days with unprecedented results.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben L et al (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376–380
Ronaghi M (2001) Pyrosequencing sheds light on DNA sequencing. Genome Res 11:3–11
Rizzi E, Lari M, Gigli E, De Bellis G, Caramelli D (2012) Ancient DNA studies: new perspectives on old samples. Genet Sel Evol 44(1):21–29
Morozova O, Hirst M, Marra M (2009) Applications of new sequencing technologies for transcriptome analysis. Annu Rev Genomics Hum Genet 10:135–151
Park PJ (2009) ChIP-seq: advantages and challenges of a maturing technology. Nat Rev Genet 10:669–680
Holt KE, Parkhill J, Mazzoni CJ, Roumagnac P, Weill F-X, Goodhead I, Rance R, Baker S, Maskell DJ, Wain J, Dolecek C, Achtman M, Dougan G (2008) High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi. Nat Genet 40:987–993
Peano C, Bicciato S, Corti G, Ferrari F, Rizzi E, Bonnal RJ, Bordoni R, Albertini A, Bernardi LR, Donadio S, De Bellis G (2007) Complete gene expression profiling of Saccharopolyspora erythraea using GeneChip DNA microarrays. Microb Cell Fact 6:37–53
Busam D, Feldblyum T, Ferriera S, Friedman R, Halpern A, Khouri H et al (2006) A Sanger/pyrosequencing hybrid approach for the generation of high-quality draft assemblies of marine microbial genomes. Proc Natl Acad Sci U S A 103:11240–11245
Fondi M, Rizzi E, Emiliani G, Orlandini V, Berna L, Papaleo MC, Perrin E, Maida I, Corti G, De Bellis G, Baldi F, Dijkshoorn L, Vaneechoutte M, Fani R (2013) The genome sequence of the hydrocarbon-degrading Acinetobacter venetianus VE-C3. Res Microbiol 164:439–449
Acknowledgements
The author acknowledges the two “FIRB-Futuro in Ricerca” grants from the Italian Minister of Education, Universities and Research (MIUR): RBFR08U07M and RBFR126B8I.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2015 Springer Science+Business Media New York
About this protocol
Cite this protocol
Rizzi, E. (2015). The Pyrosequencing Protocol for Bacterial Genomes. In: Mengoni, A., Galardini, M., Fondi, M. (eds) Bacterial Pangenomics. Methods in Molecular Biology, vol 1231. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-1720-4_4
Download citation
DOI: https://doi.org/10.1007/978-1-4939-1720-4_4
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-1719-8
Online ISBN: 978-1-4939-1720-4
eBook Packages: Springer Protocols