Uncovering Phage StrongArm: Part 3… The Final Chapter

Woah, it’s been a few months since I was last here so let me summarise what you lucky people have all missed out on. Can you believe it’s been 145 days, or 20 weeks and 5 days or 4 months and 23 days since you guys have heard from me?! Not to be exact or anything 😅 Anyways… the phage “hunt” program has FINISHED!! I know it’s sad to hear but all good things come to an end.

Sadly, I didn’t get to annotate StrongArm [1], instead he was in the very safe hands of Dr Heather Hendrickson [2]. Myself and another phriend Tyler [3] ended up helping our phriend Bailey by annotating her phage Bazzle [4]. We enjoyed our time spent with Bazzle and making a video to show people how to identify and trim tRNA’s.

The annotation process took a “tedious” amount of time, but it was still fun while it lasted. It involved using different programs called PECAAN [5], Phamerator [6] and DNA Master [7]. I know those names may be all complicated and mean nothing to you right now so let me delve into it for you guys a little bit to explain what each are used for.

PECAAN is an important program which allows you to go through each gene and choose a start and stop site and the function it may have… if it even has one. As well as being able to add and delete genes. This process used BLAST, HHPRED, GeneMark and Starterator to help figure out all of these little details, as well as using ARAGORN and tRNAscan-SE 2.0 to identify and trim tRNA’s. However, I’m not going to bore you with all the details of each one, otherwise you’ll be asleep in no time.

Figure 1. Image

Another important program used was DNA Master which helps give you more information for allowing you to choose specific start sites in closer detail by getting a representation of what each gene in the genome looks like as shown in the figure below. It also allows you to see all the coding potential and if there’s any coding regions where a new gene may be able to be added, which makes you feel awesome when you discover one!!

Figure 2. Image of an open reading frame analysis of PatrickStar from DNA Master’s quick user guide on the SEA-PHAGES website. The genes are shown here by the red and green highlights. Red is showing a reverse gene, while green shows a forward gene.

The last important program involved in annotating a phage genome is Phamerator. This allows anyone to get a good visual representation of each gene in a phages genome and how the genes differ to other phage from either different of same clusters. There is more differences between phage from different clusters than phage within the same cluster. This allows us to see the similarities and differences between phages. StrongArm is a part of the A1 cluster, while Bazzle is a part of the L2 cluster.

Figure 3. Image from Phamerator showing comparison between the genomes of Bazzle, Archie and BigCheese. It shows how similar both phage are, with only a few genes that differ in length and location. Many of the genes also belong to the same pham group, shown by the colour of each gene (e.g. gene 12 for both Bazzle, Archie and BigCheese are a part of the same pham (37389) shown by the orange colouring).

I hope this and my last two posts have helped you all get a better understanding and feel for what the whole phage “hunt” experience was like. This year has been a whirlwind of emotions from losing my first phage to finding another one. It’s been a great adventure getting to learn new things, with lots of laughs along the way. It’s sad to say goodbye as so much time and effort has been put into this that it’s like a chunk of me will be missing, but I wouldn’t trade this experience for the world.

Goodbye my phage phamily 🙂

References

1. PhagesDB: the actinobacteriophage database. (2019). Mycobacterium phage StrongArm. Retrieved from https://phagesdb.org/phages/StrongArm/

2. Massey University. (2019). Dr Heather Hendrickson. Retrieved from School of Natural and Computational Sciences – biology cluster: https://www.massey.ac.nz/massey/learning/colleges/college-of-sciences/about/natural-sciences/inms-staff/inms-biology-staff/inms-biology-staff_home.cfm?stref=953250

3. PhagesDB: the actinobacteriophage database. (2019). Mycobacterium phage Gavin. Retrieved from https://phagesdb.org/phages/Gavin/

4. PhagesDB: the actinobacteriophage database. (2019). Mycobacterium phage Bazzle. Retrieved from https://phagesdb.org/phages/Bazzle/

5. Rinehart, C. A., Gaffney, B. L., Smith, J. R., & Wood, J. D. (2016). PECAAN: User Guide [PDF file]. Retrieved from SEA-PHAGES: https://seaphages.org/media/docs/PECAAN_User_Guide_Dec7_2016.pdf

6. Cresawn, S. G., Hatfull, G. F., Bogel, M., Mavrich, T., Gauthier, C., & HHMI SEA-PHAGES. (2006-2018). Phamerator. Retrieved from http://phamerator.org

7. Lawrance, J. (2007). DNA Master. Retrieved from http://cobamide2.bio.pitt.edu/

This entry was posted in gene annotation, Phage Research, SEA-PHAGES, StrongArm and tagged , , , . Bookmark the permalink.

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