ArticleBMC genomics2013
Phage cluster relationships identified through single gene analysis.
Article in BMC genomics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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Who cites it
39 citing papers in PubMed, 54 citations in OpenAlex.
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- Genomic survey reveals no detectable bacteriophage activity in Mycobacterium bovis across a large population.FEMS microbiology ecology · 2025Article
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- Identification, Characterization, and Genome Analysis of Two Novel TemperateMicroorganisms · 2023Article
- Whole genome sequencing and annotation of a lysogenic phage vB_EcoP_DE5 isolated from donkey-derived Escherichia coli.Virus genes · 2023Article
- PCR Assay for Rapid Taxonomic Differentiation of VirulentInternational journal of molecular sciences · 2023Article
- Characterization and genomic study of EJP2, a novel jumbo phage targeting antimicrobial resistantFrontiers in microbiology · 2023Article
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- Tailed Lytic Bacteriophages of Soft Rot Pectobacteriaceae.Microorganisms · 2021Review
- Bi- and Multi-directional Gene Transfer in the Natural Populations of Polyvalent Bacteriophages, and Their Host Species Spectrum Representing Foodborne Versus Other Human and/or Animal Pathogens.Food and environmental virology · 2021Article
- Isolation, Genomic Analysis, and Preliminary Application of a BovineFrontiers in veterinary science · 2021Article
- Origin and Evolution ofMicroorganisms · 2020Article
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- A Unique Isolation of a Lytic Bacteriophage InfectedMicroorganisms · 2020Article
- Functional characterization of the endolysins derived from mycobacteriophage PDRPxv.World journal of microbiology & biotechnology · 2020Article
- Weirdo19ES is a novel singleton mycobacteriophage that selects for glycolipid deficient phage-resistant M. smegmatis mutants.PloS one · 2020Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.