ArticleVirology journal2010
The use of genomic signature distance between bacteriophages and their hosts displays evolutionary relationships and phage growth cycle determination.
Article in Virology journal, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Lifestyle shapes genome architecture and codon usage bias inFrontiers in microbiology · 2026Article
- How to introduce a new bacteriophage on the block: a short guide to phage classification.Journal of virology · 2024Review
- Inference of the Life Cycle of Environmental Phages from Genomic Signature Distances to Their Hosts.Viruses · 2023Article
- Genomic Signature in Evolutionary Biology: A Review.Biology · 2023Review
- DeePhage: distinguishing virulent and temperate phage-derived sequences in metavirome data with a deep learning approach.GigaScience · 2021Article
- Application of machine learning in bacteriophage research.BMC microbiology · 2021Review
- Genome Characterization of a Novel WastewaterFrontiers in microbiology · 2020Article
- Article
- Shigella Phages Isolated during a Dysentery Outbreak Reveal Uncommon Structures and Broad Species Diversity.Journal of virology · 2018Article
- Alignment-free $d_2^*$ oligonucleotide frequency dissimilarity measure improves prediction of hosts from metagenomically-derived viral sequences.Nucleic acids research · 2017Article
- Three novel bacteriophages isolated from the East African Rift Valley soda lakes.Virology journal · 2016Article
- Additive methods for genomic signatures.BMC bioinformatics · 2016Article
- An investigation into inter- and intragenomic variations of graphic genomic signatures.BMC bioinformatics · 2015Article
- Escherichia coli and Staphylococcus phages: effect of translation initiation efficiency on differential codon adaptation mediated by virulent and temperate lifestyles.The Journal of general virology · 2015Article
- Mapping the space of genomic signatures.PloS one · 2015Article
- Differential codon adaptation between dsDNA and ssDNA phages in Escherichia coli.Molecular biology and evolution · 2014Article
- Lateral gene transfer of family A DNA polymerases between thermophilic viruses, aquificae, and apicomplexa.Molecular biology and evolution · 2013Article
- Genome signature-based dissection of human gut metagenomes to extract subliminal viral sequences.Nature communications · 2013Article
- High diversity and novel species of Pseudomonas aeruginosa bacteriophages.Applied and environmental microbiology · 2012Article
- Microbial lifestyle and genome signatures.Current genomics · 2012Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundBacteriophage classification is mainly based on morphological traits and genome characteristics combined with host information and in some cases on phage growth lifestyle. A lack of molecular tools can impede more precise studies on phylogenetic relationships or even a taxonomic classification. The use of methods to analyze genome sequences without the requirement for homology has allowed advances in classification.
resultsHere, we proposed to use genome sequence signature to characterize bacteriophages and to compare them to their host genome signature in order to obtain host-phage relationships and information on their lifestyle. We analyze the host-phage relationships in the four most representative groups of Caudoviridae, the dsDNA group of phages. We demonstrate that the use of phage genomic signature and its comparison with that of the host allows a grouping of phages and is also able to predict the host-phage relationships (lytic vs. temperate).
conclusionsWe can thus condense, in relatively simple figures, this phage information dispersed over many publications.
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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.