Viral adaption of staphylococcal phage: A genome-based analysis of the selective preference based on codon usage Bias.
Genome evolution
Host limitation
Phagic phenotype
Staphylococcal phage
Synonymous codon usage
Journal
Genomics
ISSN: 1089-8646
Titre abrégé: Genomics
Pays: United States
ID NLM: 8800135
Informations de publication
Date de publication:
11 2020
11 2020
Historique:
received:
04
03
2020
revised:
19
07
2020
accepted:
11
08
2020
pubmed:
21
8
2020
medline:
14
9
2021
entrez:
21
8
2020
Statut:
ppublish
Résumé
Given the high therapeutic value of the staphylococcal phage, the genome co-evolution of the phage and the host has gained great attention. Though the genome-wide AT richness in staphylococcal phages has been well-studied with nucleotide usage bias, here we proved that host factor, lifestyle and taxonomy are also important factors in understanding the phage nucleotide usages bias using information entropy formula. Such correlation is especially prominent when it comes to the synonymous codon usages of staphylococcal phages, despite the overall scattered codon usage pattern represented by principal component analysis. This strong relationship is explained by nucleotide skew which testified that the usage biases of nucleotide at different codon positions are acting on synonymous codons. Therefore, our study reveals a hidden relationship of genome evolution with host limitation and phagic phenotype, providing new insight into phage genome evolution at genetic level.
Identifiants
pubmed: 32818632
pii: S0888-7543(20)30216-0
doi: 10.1016/j.ygeno.2020.08.012
pii:
doi:
Substances chimiques
Nucleotides
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
4657-4665Informations de copyright
Copyright © 2020 Elsevier Inc. All rights reserved.