Abstract and Final Data Collection

Date: 4-19-19

• Rationale
  • The rational for this lab is to finish gathering data to use for our independent research project as well as write an abstract for the project.
• Procedure
  1. DNAMaster was used to determine the start codon used for each gene by each phage in the AU cluster.
  2. Findings were recorded on a Google Sheets page and tendencies were calculated.
  3. The group worked together on a abstract for the project, functioning as a summary and introduction to our research.
• Results
  • Start codons are nucleotide sequences that are found at the beginning of protein-coding genes of DNA. In bacteriophage, these start with the base pairs ATG, GTG, or TTG. Generally, ATG and GTG codons are used at the same frequency, and TTG is used in 7% of cases. This study aims to discover trends between this start-codon tendency and evolutionary relationships between phages within the clusters AM, AQ, AR, and AU. As phage genomics is a recently repopularized field, not much is known about them or how they work. If trends like these are discovered, we can more easily characterize and group phages into subclusters, which in turn would allow future analysts to perform more focused research. Data was gathered using the database PhagesDB and was recorded and expressed using Microsoft Excel, DNAMaster, and SplitsTree4. Start codon preferences were calculated on a spreadsheet and compared to the unrooted phylogenetic trees created with SplitsTree. Our results were inconclusive in regard to a trend between start-codon preferences and evolutionary relatedness being useful as subclustering criteria. However, an interesting trend was discovered in the clusters studied. In each cluster, there is a cluster-specific, highly conserved pattern of start-codon usage at specific locations within the genome that span four to five genes. Although our results were inconclusive, if a study were to recreate ours with data analysis focused on phage within a chosen geographical area, it’s possible that a trend could emerge between start-codon tendency and relationships of phages discovered in this close proximity.
  • The following is an example of the start codons used by CapnMurica, an AU phage.
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• Future Plans
  • The next step is to continue to compare the data we’ve collected and search for trends or surprising discoveries.