Abstract
High-throughput sequencing (HTS) is an effective tool for bacteriophage genome and its termini analysis. HTS technology parallelizes the sequencing process, producing thousands to millions of reads concurrently. Terminal information of a bacteriophage genome is important and basic knowledge for understanding the biology of the bacteriophage. We have created a high-occurrence reads as termini theory and developed practical methods to determine the bacteriophage genome termini, which is based on the large data of HTS. With this method, the termini of the bacteriophage genome can be efficiently and reliably identified as a by-product of bacteriophage genome sequencing, by solely analyzing the sequence statistics of the raw sequencing data (reads), without any further lab experiments.
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
Hershey AD, Chase M (1952) Independent functions of viral protein and nucleic acid in growth of bacteriophage. J Gen Physiol 36(1):39–56
McKenna M (2014) Drugs: gut response. Nature 508(7495):182–183
Li S, Fan H, An X, Fan H, Jiang H, Chen Y, Tong Y (2014) Scrutinizing virus genome termini by high-throughput sequencing. PLoS One 9(1):e85806
Adams MH (1959) Bacteriophages. Bacteriophages
Carlson K (2005) Appendix: working with bacteriophages: common techniques and methodological approaches. Bacteriophages:437–494
Green MR, Sambrook J (2012) Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory Press, New York
Loman NJ, Misra RV, Dallman TJ, Constantinidou C, Gharbia SE, Wain J, Pallen MJ (2012) Performance comparison of benchtop high-throughput sequencing platforms. Nat Biotechnol 30(5):434–439
Pennisi E (2010) Semiconductors inspire new sequencing technologies. Science 327(5970):1190–1190
Zhang J, Chiodini R, Badr A, Zhang G (2011) The impact of next-generation sequencing on genomics. J Genet Genomics 38(3):95–109
Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, Hall KP, Evers DJ, Barnes CL, Bignell HR (2008) Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456(7218):53–59
Lu S, Le S, Tan Y, Zhu J, Li M, Rao X, Zou L, Li S, Wang J, Jin X (2013) Genomic and proteomic analyses of the terminally redundant genome of the Pseudomonas aeruginosa phage PaP1: establishment of genus PaP1-like phages. PLoS One 8(5):e62933
Zerbino DR, Birney E (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18(5):821–829
Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol I (2009) ABySS: a parallel assembler for short read sequence data. Genome Res 19(6):1117–1123
Li R, Li Y, Kristiansen K, Wang J (2008) SOAP: short oligonucleotide alignment program. Bioinformatics 24(5):713–714
Gordon A (2011) FASTX-Toolkit. Hannon Lab. http://hannonlab.cshl.edu/fastx_toolkit/index.html. Accessed 26 Nov 2014
NCBI (2014.) Nucleotide Blast http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome. Accessed 26 Nov 2014
Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M (2008) The RAST server: rapid annotations using subsystems technology. BMC Genomics 9(1):75
Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25(5):0955–0964
Jiang X, Jiang H, Li C, Wang S, Mi Z, An X, Chen J, Tong Y (2011) Sequence characteristics of T4-like bacteriophage IME08 benome termini revealed by high throughput sequencing. Virol J 8:194
Sheng W, Huanhuan J, Jiankui C, Dabin L, Cun L, Bo P, Xiaoping A, Xin Z, Yusen Z, Yigang T (2010) Isolation and rapid genetic characterization of a novel T4-like bacteriophage. J Med Coll PLA 25(6):331–340
Crooks GE, Hon G, Chandonia J-M, Brenner SE (2004) WebLogo: a sequence logo generator. Genome Res 14(6):1188–1190
Zhang X, Wang Y, Li S et al. (2015) A novel termini analysis theory using HTS data alone for the identification of Enterococcus phage EF4-like genome termini. BMC Genomics 16(414): DOI 10.1186/s12864-015-1612-3
Wang Y, Wang W, Lv Y, Zheng W, Mi Z, Pei G, An X, Xu X, Han C, Liu J (2014) Characterization and complete genome sequence analysis of novel bacteriophage IME-EFm1 infecting enterococcus faecium. J Gen Virol 95(Pt 11):2565–2575
Zhang X, Kang H, Li Y et al. (2015) Conserved termini and adjacent variable region of Twortlikevirus Staphylococcus phages. Virologica Sinica 30(6):433–440
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2018 Springer Science+Business Media LLC
About this protocol
Cite this protocol
Zhang, X., Wang, Y., Tong, Y. (2018). Analyzing Genome Termini of Bacteriophage Through High-Throughput Sequencing. 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_11
Download citation
DOI: https://doi.org/10.1007/978-1-4939-7343-9_11
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