Abstract
BackgroundPhylogenetic comparison of bacteriophages requires whole genome approaches such as dotplot analysis, genome pairwise maps, and gene content analysis. Currently mycobacteriophages, a highly studied phage group, are categorized into related clusters based on the comparative analysis of whole genome sequences. With the recent explosion of phage isolation, a simple method for phage cluster prediction would facilitate analysis of crude or complex samples without whole genome isolation and sequencing. The hypothesis of this study was that mycobacteriophage-cluster prediction is possible using comparison of a single, ubiquitous, semi-conserved gene. Tape Measure Protein (TMP) was selected to test the hypothesis because it is typically the longest gene in mycobacteriophage genomes and because regions within the TMP gene are conserved.ResultsA single gene, TMP, identified the known Mycobacteriophage clusters and subclusters using a Gepard dotplot comparison or a phylogenetic tree constructed from global alignment and maximum likelihood comparisons. Gepard analysis of 247 mycobacteriophage TMP sequences appropriately recovered 98.8% of the subcluster assignments that were made by whole-genome comparison. Subcluster-specific primers within TMP allow for PCR determination of the mycobacteriophage subcluster from DNA samples. Using the single-gene comparison approach for siphovirus coliphages, phage groupings by TMP comparison reflected relationships observed in a whole genome dotplot comparison and confirm the potential utility of this approach to another widely studied group of phages.ConclusionsTMP sequence comparison and PCR results support the hypothesis that a single gene can be used for distinguishing phage cluster and subcluster assignments. TMP single-gene analysis can quickly and accurately aid in mycobacteriophage classification.
Highlights
Phylogenetic comparison of bacteriophages requires whole genome approaches such as dotplot analysis, genome pairwise maps, and gene content analysis
This study demonstrates that a single gene can group mycobacteriophages into the same clusters and subclusters proposed by whole genome dotplot analysis
The Tape Measure Protein (TMP; [9,10]) which is typically encoded by the longest gene of a phage genome was selected, and the nucleotide and amino acid sequences of TMP were analyzed in 247 mycobacteriophages representing more than 42 subclusters
Summary
Phylogenetic comparison of bacteriophages requires whole genome approaches such as dotplot analysis, genome pairwise maps, and gene content analysis. A highly studied phage group, are categorized into related clusters based on the comparative analysis of whole genome sequences. For mycobacteriophage cluster and subcluster assignment, whole genomes are currently compared primarily by dotplot, but pairwise average nucleotide identities (ANI), pairwise genome maps, and gene content analysis are all considered [7]. This study demonstrates that a single gene can group mycobacteriophages into the same clusters and subclusters proposed by whole genome dotplot analysis. The Tape Measure Protein (TMP; [9,10]) which is typically encoded by the longest gene of a phage genome was selected, and the nucleotide and amino acid sequences of TMP were analyzed in 247 mycobacteriophages representing more than 42 subclusters. Due to the highly mosaic nature of phages, subsequent full genome sequence analysis is appropriate to ensure proper taxonomic assignment reflecting the complex evolutionary history of the phages
Sign-in/Register to view highlights & summary 
Published Version (
Free)
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call