A probably silly question to phage experts.
Is it possible to determine whether a phage genome is linear, circular, or circularly permutated using Illumina sequencing data and genome assembly? Thank you very much!
I would imagine that a linear genome would appear linear upon assembly and analysis but both circular or circularly permuted would appear as circular (this is of course presuming sufficient depth of coverage of a population of molecules).
Greetings,
Elucidation of the exact genome termini is what you probably want.
I've found PhageTerm (Garneau et al., 2017) to be a great tool to have an automated look at the phage read pile-ups onto the scaffold representing phage complete genome for termini determination, which works well with paired reads when the library prep involved random physical shearing (we usually use TruSeq DNA Nano workflow with shearing by Covaris ultrasonication; however, it won't be suitable for Nextera-prepared libraries, which is a very common library prep choice). Even in case of lackluster coverage, read pile-up inspection and TerL aa sequence tree generation with your phage TerL sequence and other TerL sequences from phages that had their termini elucidated experimentally (not only in silico) can usually aid in the proper in vitro experiment design (have a look at Casjens et al., 2009) to verify/find out the packaging strategy/termini phage has.
Best regards,
Nikita Zrelovs
1. Garneau, J.R., Depardieu, F., Fortier, LC. et al. PhageTerm: a tool for fast and accurate determination of phage termini and packaging mechanism using next-generation sequencing data. Sci Rep 7, 8292 (2017). https://doi.org/10.1038/s41598-017-07910-5
2. Casjens, Sherwood R, and Eddie B Gilcrease. “Determining DNA packaging strategy by analysis of the termini of the chromosomes in tailed-bacteriophage virions.” Methods in molecular biology (Clifton, N.J.) vol. 502 (2009): 91-111. doi:10.1007/978-1-60327-565-1_7
- Badges
- Science topic
- Similar topics
- Biological Science
- Molecular Biology
- Molecular Methods
- Cloning