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Bacteriophages pp 231–238Cite as

Phage Genome Annotation Using the RAST Pipeline

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

Abstract

Phages are complex biomolecular machineries that have to survive in a bacterial world. Phage genomes show many adaptations to their lifestyle such as shorter genes, reduced capacity for redundant DNA sequences, and the inclusion of tRNAs in their genomes. In addition, phages are not free-living, they require a host for replication and survival. These unique adaptations provide challenges for the bioinformatics analysis of phage genomes. In particular, ORF calling, genome annotation, noncoding RNA (ncRNA) identification, and the identification of transposons and insertions are all complicated in phage genome analysis. We provide a road map through the phage genome annotation pipeline, and discuss the challenges and solutions for phage genome annotation as we have implemented in the rapid annotation using subsystems (RAST) pipeline.

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References

  1. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O (2008) The RAST Server: rapid annotations using subsystems technology. BMC Genomics 9:75

    Article  PubMed  PubMed Central  Google Scholar 

  2. Brettin T, Davis JJ, Disz T, Edwards RA, Gerdes S, Olsen GJ, Olson R, Overbeek R, Parrello B, Pusch GD, Shukla M, Thomason Iii JA, Stevens R, Vonstein V, Wattam AR, Xia F (2015) RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci Rep 5:8365

    Article  PubMed  PubMed Central  Google Scholar 

  3. Badger JH, Olsen GJ (1999) CRITICA: coding region identification tool invoking comparative analysis. Mol Biol Evol 16:512–524

    Article  CAS  PubMed  Google Scholar 

  4. Borodovsky M, Mclninch JD, Koonin EV, Rudd KE, Médigue C, Danchin A (1995) Detection of new genes in a bacterial genome using Markov models for three gene classes. Nucleic Acids Res 23:3554–3562

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Lukashin AV, Borodovsky M (1998) GeneMark.hmm: new solutions for gene finding. Nucleic Acids Res 26:1107–1115

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Krause L, McHardy AC, Pühler A, Stoye J, Meyer F (2007) GISMO - Gene identification using a support vector machine for ORF classification. Nucleic Acids Res 35:540–549

    Article  CAS  PubMed  Google Scholar 

  7. Delcher AL, Harmon D, Kasif S, White O, Salzberg SL (1999) Improved microbial gene identification with GLIMMER. Nucleic Acids Res 27:4636–4641

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Kelley DR, Liu B, Delcher AL, Pop M, Salzberg SL (2012) Gene prediction with Glimmer for metagenomic sequences augmented by classification and clustering. Nucleic Acids Res 40:e9–e9

    Article  CAS  PubMed  Google Scholar 

  9. Noguchi H, Taniguchi T, Itoh T (2008) MetaGeneAnnotator: Detecting species-specific patterns of ribosomal binding site for precise gene prediction in anonymous prokaryotic and phage genomes. DNA Res 15:387–396

    Google Scholar 

  10. Hyatt D, Chen G-L, LoCascio PF, Land ML, Larimer FW, Hauser LJ (2010) Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11:119

    Article  PubMed  PubMed Central  Google Scholar 

  11. Summer EJ, Berry J, Tran TAT, Niu L, Struck DK, Young R (2007) Rz/Rz1 lysis gene equivalents in phages of Gram-negative hosts. J Mol Biol 373:1098–1112

    Article  CAS  PubMed  Google Scholar 

  12. Walker PJ, Firth C, Widen SG, Blasdell KR, Guzman H, Wood TG, Paradkar PN, Holmes EC, Tesh RB, Vasilakis N (2015) Evolution of genome size and complexity in the Rhabdoviridae. PLoS Pathog 11:e1004664

    Article  PubMed  PubMed Central  Google Scholar 

  13. Kristensen DM, Waller AS, Yamada T, Bork P, Mushegian AR, Koonin EV (2013) Orthologous gene clusters and taxon signature genes for viruses of prokaryotes. J Bacteriol 195:941–950

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. McNair K, Bailey BA, Edwards RA (2012) PHACTS, a computational approach to classifying the lifestyle of phages. Bioinformatics 28:614–618

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Seguritan V, Alves N, Arnoult M, Raymond A, Lorimer D, Burgin AB, Salamon P, Segall AM (2012) Artificial neural networks trained to detect viral and phage structural proteins. PLoS Comput Biol 8:e1002657

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25:955–964

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Nawrocki EP (2014) Annotating functional RNAs in genomes using Infernal. Methods Mol Biol 1097:163–197

    Article  CAS  PubMed  Google Scholar 

  18. Bailly-Bechet M, Vergassola M, Rocha E (2007) Causes for the intriguing presence of tRNAs in phages. Genome Res 17:1486–1495

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Williams KP (2002) Integration sites for genetic elements in prokaryotic tRNA and tmRNA genes: sublocation preference of integrase subfamilies. Nucleic Acids Res 30:866–875

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Seed KD, Lazinski DW, Calderwood SB, Camilli A (2013) A bacteriophage encodes its own CRISPR/Cas adaptive response to evade host innate immunity. Nature 494:489–491

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Cassman N, Prieto-Davó A, Walsh K, Silva GGZ, Angly F, Akhter S, Barott K, Busch J, McDole T, Haggerty JM, Willner D, Alarcón G, Ulloa O, DeLong EF, Dutilh BE, Rohwer F, Dinsdale EA (2012) Oxygen minimum zones harbour novel viral communities with low diversity. Environ Microbiol 14:3043–3065

    Article  CAS  PubMed  Google Scholar 

  22. Aziz RK, Breitbart M, Edwards RA (2010) Transposases are the most abundant, most ubiquitous genes in nature. Nucleic Acids Res 38:4207–4217

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Riadi G, Medina-Moenne C, Holmes DS (2012) TnpPred: a web service for the robust prediction of prokaryotic transposases. Comp Funct Genomics 2012:678761

    Article  PubMed  PubMed Central  Google Scholar 

  24. Benson G (1999) Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res 27:573–580

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Volfovsky N, Haas BJ, Salzberg SL (2001) A clustering method for repeat analysis in DNA sequences. Genome Biol 2:RESEARCH0027

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Kropinski AM, Prangishvili D, Lavigne R (2009) Position paper: the creation of a rational scheme for the nomenclature of viruses of Bacteria and Archaea. Environ Microbiol 11:2775–2777

    Article  PubMed  Google Scholar 

  27. Edwards RA, McNair K, Faust K, Raes J, Dutilh BE (2016) Computational approaches to predict bacteriophage–host relationships. FEMS Microbiol Rev 40:58–72

    Article  Google Scholar 

  28. Aziz RK, Dwivedi B, Akhter S, Breitbart M, Edwards RA (2015) Multidimensional metrics for estimating phage abundance, distribution, gene density, and sequence coverage in metagenomes. Front Microbiol 6:381

    PubMed  PubMed Central  Google Scholar 

  29. Akhter S, Aziz RK, Edwards RA (2012) PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies. Nucleic Acids Res 40:e126–e126

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Akhter S, Bailey BA, Salamon P, Aziz RK, Edwards RA (2013) Applying Shannon’s information theory to bacterial and phage genomes and metagenomes. Sci Rep 3:1033

    Article  PubMed  PubMed Central  Google Scholar 

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Acknowledgments

This work was supported by grants from the National Science Foundation MCB-1330800 and DUE-1323809 to RAE. BED was supported by the Netherlands Organization for Scientific Research (NWO) Vidi grant 864.14.004.

Author information

Authors and Affiliations

  1. Computational Sciences Research Center, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182, USA

    Katelyn McNair & Robert Edwards

  2. Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, 11562, Egypt

    Ramy Karam Aziz

  3. Argonne National Laboratory, 9700 S. Cass Ave, Argonne, IL, 60439, USA

    Ramy Karam Aziz, Gordon D. Pusch & Ross Overbeek

  4. Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8, 3584, Utrecht, The Netherlands

    Bas E. Dutilh

  5. Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Geert Grooteplein 28, 6525, Nijmegen, The Netherlands

    Bas E. Dutilh

  6. Departments of Biology and Computer Science, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182, USA

    Robert Edwards

Authors
  1. Katelyn McNair
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  2. Ramy Karam Aziz
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  3. Gordon D. Pusch
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  4. Ross Overbeek
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  5. Bas E. Dutilh
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  6. Robert Edwards
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Corresponding author

Correspondence to Robert Edwards .

Editor information

Editors and Affiliations

  1. Department Infection, Immunity & Inflammation, University of Leicester School of Medicine, Leicester, United Kingdom

    Martha R.J. Clokie

  2. University of Guelph, Guelph, Ontario, Canada

    Andrew M. Kropinski

  3. KU Leuven, Laboratory of Gene Technology, Leuven, Belgium

    Rob Lavigne

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McNair, K., Aziz, R.K., Pusch, G.D., Overbeek, R., Dutilh, B.E., Edwards, R. (2018). Phage Genome Annotation Using the RAST Pipeline. 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_17

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  • DOI: https://doi.org/10.1007/978-1-4939-7343-9_17

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  • 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

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