ArticleBMC genomics2015
A novel termini analysis theory using HTS data alone for the identification of Enterococcus phage EF4-like genome termini.
Article in BMC genomics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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20 citing papers in PubMed, 32 citations in OpenAlex.
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- Temporal transcriptomes of a marine cyanopodovirus and its Synechococcus host during infection.MicrobiologyOpen · 2021Article
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- Biological characteristics and genome analysis of a novel phage vB_KpnP_IME279 infecting Klebsiella pneumoniae.Folia microbiologica · 2020Article
- A novel freshwater cyanophage vB_MelS-Me-ZS1 infecting bloom-forming cyanobacterium Microcystis elabens.Molecular biology reports · 2020Article
- Isolation and Characterization of a Novel Bacteriophage Infecting Carbapenem-Resistant Klebsiella pneumoniae.Current microbiology · 2020Article
- A Novel Benthic Phage InfectingViruses · 2019Article
- PhageTerm: a tool for fast and accurate determination of phage termini and packaging mechanism using next-generation sequencing data.Scientific reports · 2017Article
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- Predicting genome terminus sequences of Bacillus cereus-group bacteriophage using next generation sequencing data.BMC genomics · 2017Article
- Conserved termini and adjacent variable region of Twortlikevirus Staphylococcus phages.Virologica Sinica · 2015Article
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Authors and funding
12 authors at 4 institutions in 2 countries.
Funding
Abstract
backgroundEnterococcus faecalis and Enterococcus faecium are typical enterococcal bacterial pathogens. Antibiotic resistance means that the identification of novel E. faecalis and E. faecium phages against antibiotic-resistant Enterococcus have an important impact on public health. In this study, the E. faecalis phage IME-EF4, E. faecium phage IME-EFm1, and both their hosts were antibiotic resistant. To characterize the genome termini of these two phages, a termini analysis theory was developed to provide a wealth of terminal sequence information directly, using only high-throughput sequencing (HTS) read frequency statistics.
resultsThe complete genome sequences of phages IME-EF4 and IME-EFm1 were determined, and our termini analysis theory was used to determine the genome termini of these two phages. Results showed 9 bp 3' protruding cohesive ends in both IME-EF4 and IME-EFm1 genomes by analyzing frequencies of HTS reads. For the positive strands of their genomes, the 9 nt 3' protruding cohesive ends are 5'-TCATCACCG-3' (IME-EF4) and 5'-GGGTCAGCG-3' (IME-EFm1). Further experiments confirmed these results. These experiments included mega-primer polymerase chain reaction sequencing, terminal run-off sequencing, and adaptor ligation followed by run-off sequencing.
conclusionUsing this termini analysis theory, the termini of two newly isolated antibiotic-resistant Enterococcus phages, IME-EF4 and IME-EFm1, were identified as the byproduct of HTS. Molecular biology experiments confirmed the identification. Because it does not require time-consuming wet lab termini analysis experiments, the termini analysis theory is a fast and easy means of identifying phage DNA genome termini using HTS read frequency statistics alone. It may aid understanding of phage DNA packaging.
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