Skip to main content

Amplification for Whole Genome Sequencing of Bacteriophages from Single Isolated Plaques Using SISPA

  • Protocol
  • First Online:
Bacteriophages

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1681))

Abstract

Genomics has greatly transformed our understanding of phage biology; however, traditional methods of DNA isolation for whole genome sequencing have required phages to be grown to high titers in large-scale preparations, potentially selecting for only those phages that can grow efficiently under laboratory conditions. This may also select for mutations or deletions that enable more efficient growth in culture. The ability to sequence a bacteriophage genome from a single isolated plaque reduces these risks while decreasing the time and complexity of bacteriophage genome sequencing. A method of amplification and library preparation is described, utilizing Sequence Independent Single Primer Amplification (SISPA), that can be used for whole genome shotgun sequencing of bacteriophages from a single isolated plaque.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 79.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 99.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 129.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Allander T, Emerson SU, Engle RE, Purcell RH, Bukh J (2001) A virus discovery method incorporating DNase treatment and its application to the identification of two bovine parvovirus species. Proc Natl Acad Sci U S A 98(20):11609–11614

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Breitbart M, Rohwer F (2005) Method for discovering novel DNA viruses in blood using viral particle selection and shotgun sequencing. Biotechniques 39(5):729–736

    Article  CAS  PubMed  Google Scholar 

  3. van der Hoek L, Pyrc K, Jebbink MF, Vermeulen-Oost W, Berkhout RJ, Wolthers KC et al (2004) Identification of a new human coronavirus. Nat Med 10(4):368–373

    Article  PubMed  Google Scholar 

  4. Jones MS, Kapoor A, Lukashov VV, Simmonds P, Hecht F, Delwart E (2005) New DNA viruses identified in patients with acute viral infection syndrome. J Virol 79(13):8230–8236

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Palmenberg AC, Spiro D, Kuzmickas R, Wang S, Djikeng A, Rathe JA et al (2009) Sequencing and analyses of all known human rhinovirus genomes reveal structure and evolution. Science 324(5923):55–59

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Djikeng A, Halpin R, Kuzmickas R, Depasse J, Feldblyum J, Sengamalay N et al (2008) Viral genome sequencing by random priming methods. BMC Genomics 9:5

    Article  PubMed  PubMed Central  Google Scholar 

  7. Agindotan BO, Ahonsi MO, Domier LL, Gray ME, Bradley CA (2010) Application of sequence-independent amplification (SIA) for the identification of RNA viruses in bioenergy crops. J Virol Methods 169(1):119–128

    Article  CAS  PubMed  Google Scholar 

  8. Victoria JG, Kapoor A, Dupuis K, Schnurr DP, Delwart EL (2008) Rapid identification of known and new RNA viruses from animal tissues. PLoS Pathog 4(9):e1000163

    Article  PubMed  PubMed Central  Google Scholar 

  9. Froussard P (1992) A random-PCR method (rPCR) to construct whole cDNA library from low amounts of RNA. Nucleic Acids Res 20(11):2900

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Depew J, Zhou B, McCorrison JM, Wentworth DE, Purushe J, Koroleva G et al (2013) Sequencing viral genomes from a single isolated plaque. Virol J 10:181

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Reyes GR, Kim JP (1991) Sequence-independent, single-primer amplification (SISPA) of complex DNA populations. Mol Cell Probes 5(6):473–481

    Article  CAS  PubMed  Google Scholar 

  12. Moser LA, Ramirez-Carvajal L, Puri V, Pauszek SJ, Matthews K, Dilley KA et al (2016) A universal next-generation sequencing protocol to generate noninfectious barcoded cdna libraries from high-containment rna viruses. mSystems 1(3):e00039

    Article  PubMed  PubMed Central  Google Scholar 

  13. Wright MS, Stockwell TB, Beck E, Busam DA, Bajaksouzian S, Jacobs MR et al (2015) SISPA-Seq for rapid whole genome surveys of bacterial isolates. Infect Genet Evol 32:191–198

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Gaillard C, Strauss F (1990) Ethanol precipitation of DNA with linear polyacrylamide as carrier. Nucleic Acids Res 18(2):378

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Hartley JL, Bowen H (1996) PEG precipitation for selective removal of small DNA fragments. Focus 18(1):27

    Google Scholar 

  16. Hall RJ, Wang J, Todd AK, Bissielo AB, Yen S, Strydom H et al (2014) Evaluation of rapid and simple techniques for the enrichment of viruses prior to metagenomic virus discovery. J Virol Methods 195:194–204

    Article  CAS  PubMed  Google Scholar 

  17. Bartram A, Poon C, Neufeld J (2009) Nucleic acid contamination of glycogen used in nucleic acid precipitation and assessment of linear polyacrylamide as an alternative co-precipitant. Biotechniques 47(6):1019–1022

    Article  CAS  PubMed  Google Scholar 

  18. Frackman S, Kobs G, Simpson D, Storts D (1998) Betaine and DMSO: Enhancing Agents for PCR. Promega Notes 65:27–30

    Google Scholar 

Download references

Acknowledgments

The author wishes to thank Galina Koroleva, Jessica DePew, Janaki Purushe, Bin Zhou, and Manolito Torralba for their contributions to the development of these protocols. This work was supported with funds from the United States National Institutes of Health (R21-DE018063 and U54-AI84844) and in part with funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services under contract number HHSN272200900007C.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Derick E. Fouts .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2018 Springer Science+Business Media LLC

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

Fouts, D.E. (2018). Amplification for Whole Genome Sequencing of Bacteriophages from Single Isolated Plaques Using SISPA. In: Clokie, M., Kropinski, A., Lavigne, R. (eds) Bacteriophages. Methods in Molecular Biology, vol 1681. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7343-9_12

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-7343-9_12

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7341-5

  • Online ISBN: 978-1-4939-7343-9

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics