Jess Hastings

Date of Work: 3/28/2017

Rationale: The purpose of this lab was to begin continue working on our research project and begin collecting information. In order to do this, our research question has to be clearly defined and a plan of action for the project must be outlined.

Methods: 

1. Identify two other clusters that have myovirdae morphology
2. Identify two published phage genomes within those two clusters
3. Identify the tape measure gene in each genome and obtain nucleotide sequence
4. Run an NCBI Blast to see similarity between tape measure genes in the same cluster

 Tools used: DNAMaster, Phamerator, NCBI Blast

Results:

The two clusters that contained myovirdae phages that were used were the AM and AK clusters.

The AM cluster only contains 1 published genome, Circum. While we were unable to compare this sequence with another AM phage to see similarity, the sequence will be used when comparing the different clusters.

Figure 1: NCBI Blast Results – Circum (AM)

Within the AK cluster the phages Bennie and Greenhouse were compared. When comparing the nucleotide sequence of these two phages tape measure genes they were found to have a 93% similarity. This is lower than the 99% similarity that was found between AN phages, but is still a high match.

Figure 2: NCBI Blast results for Bennie (93% match with Greenhouse)

By comparing these two phages in the the AK cluster, we were able to confirm that tape measure genes within a cluster share similarities in nucleotide sequence. With this understand, we then moved next to comparing the different clusters to see if there was any similarity in their tape measure genes.

Conclusions:

The results found during lab confirmed multiple questions in our research project. By comparing the sequences of two AK cluster, we found that they also share a high amount of similarity, as expected. This is expected because phages are put into clusters based upon genome similarity. Also, these two phages are of the same morphology. This matters because the tape measure protein is directly related to the length of the phages tail. We wanted to be sure to compare two different phages that have the same morphology because each morphology is known for having an average length of tail.

Future Plans:

After gathering all the nucleotide sequences from three different clusters and comparing their similarity with the cluster, we will now compare the three different clusters against each other. While we expect there to be some difference in the nucleotide sequence because they are from different clusters we also expect there to be some similarities. This is expected because the phages are of the same morphology which means that they all have a similar average tail length which is determined by the length of the tape measure protein.