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Open Access Research article

Phage cluster relationships identified through single gene analysis

Kyle C Smith1, Eduardo Castro-Nallar2, Joshua NB Fisher1, Donald P Breakwell1*, Julianne H Grose1* and Sandra H Burnett1*

Author Affiliations

1 Microbiology and Molecular Biology Department, Brigham Young University, Provo, UT, USA

2 Computational Biology Institute, George Washington University, Ashburn, VA, USA

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BMC Genomics 2013, 14:410  doi:10.1186/1471-2164-14-410

Published: 19 June 2013

Abstract

Background

Phylogenetic 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.

Results

A 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.

Conclusions

TMP 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.

Keywords:
Mycobacteriophage; Coliphage; Cluster; Subcluster; Phylogeny; PCR; FFP; Phage genomics