ArticleBacteriophage2011
Single-stranded genomic architecture constrains optimal codon usage.
Article in Bacteriophage, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
19 citing papers in PubMed, 27 citations in OpenAlex.
- Genome Characterization of Temperate Bacteriophages and Associated Genetic Features in Avian PathogenicAnimals : an open access journal from MDPI · 2026Article
- Contrasting genome composition and codon usage inVirus evolution · 2026Article
- Activity of novel virus families infecting soil nitrifiers is concomitant with host niche differentiation.The ISME journal · 2024Article
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- Propagation of viral genomes by replicating ammonia-oxidising archaea during soil nitrification.The ISME journal · 2023Article
- Widespread, human-associated redondoviruses infect the commensal protozoan Entamoeba gingivalis.Cell host & microbe · 2023Article
- VEBA: a modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes.BMC bioinformatics · 2022Article
- Prophage Diversity AcrossFrontiers in microbiology · 2022Article
- The Dynamic Codon Biaser: calculating prokaryotic codon usage biases.Microbial genomics · 2021Article
- Entamoeba and Giardia parasites implicated as hosts of CRESS viruses.Nature communications · 2020Article
- Identification of a novel archaea virus, detected in hydrocarbon polluted Hungarian and Canadian samples.PloS one · 2020Article
- Universal evolutionary selection for high dimensional silent patterns of information hidden in the redundancy of viral genetic code.Bioinformatics (Oxford, England) · 2018Article
- Comparative genomic analysis ofGut pathogens · 2017Article
- Linking Virus Genomes with Host Taxonomy.Viruses · 2016Article
- Viral dark matter and virus-host interactions resolved from publicly available microbial genomes.eLife · 2015Article
- System analysis of synonymous codon usage biases in archaeal virus genomes.Journal of theoretical biology · 2014Article
- Differential codon adaptation between dsDNA and ssDNA phages in Escherichia coli.Molecular biology and evolution · 2014Article
- Base composition and translational selection are insufficient to explain codon usage bias in plant viruses.Viruses · 2013Article
- Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Viral codon usage is shaped by the conflicting forces of mutational pressure and selection to match host patterns for optimal expression. We examined whether genomic architecture (single- or double-stranded DNA) influences the degree to which bacteriophage codon usage differ from their primary bacterial hosts and each other. While both correlated equally with their hosts' genomic nucleotide content, the coat genes of ssDNA phages were less well adapted than those of dsDNA phages to their hosts' codon usage profiles due to their preference for codons ending in thymine. No specific biases were detected in dsDNA phage genomes. In all nine of ten cases of codon redundancy in which a specific codon was overrepresented, ssDNA phages favored the NNT codon. A cytosine to thymine biased mutational pressure working in conjunction with strong selection against non-synonymous mutations appears be shaping codon usage bias in ssDNA viral genomes.
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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.