Single-stranded genomic architecture constrains optimal codon usage.

Bacteriophage
Daniel J Cardinale, Siobain Duffy

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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Citations

Mar 4, 2014·Molecular Biology and Evolution·Shivapriya ChithambaramXuhua Xia
Mar 5, 2016·Viruses·Tomoko MiharaHiroyuki Ogata
Apr 2, 2014·Journal of Theoretical Biology·Sen Li, Jie Yang
Sep 17, 2020·Nature Communications·Cormac M KinsellaLia van der Hoek
Oct 27, 2021·Microbial Genomics·Brian DehlingerCatherine Putonti

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