Codon usage pattern and its influencing factors in different genomes of hepadnaviruses.
Journal
Archives of virology
ISSN: 1432-8798
Titre abrégé: Arch Virol
Pays: Austria
ID NLM: 7506870
Informations de publication
Date de publication:
Mar 2020
Mar 2020
Historique:
received:
31
08
2019
accepted:
07
12
2019
pubmed:
10
2
2020
medline:
23
2
2020
entrez:
10
2
2020
Statut:
ppublish
Résumé
Codon usage bias (CUB) arises from the preference for a codon over codons for the same amino acid. The major factors contributing to CUB are evolutionary forces, compositional properties, gene expression, and protein properties. The present analysis was performed to investigate the compositional properties and the extent of CUB across the genomes of members of the family Hepadnaviridae, as previously no work using bioinformatic tools has been reported. The viral genes were found to be AT rich with low CUB. Analysis of relative synonymous codon usage (RSCU) was used to identify overrepresented and underrepresented codons for each amino acid. Correlation analysis of overall nucleotide composition and its composition at the third codon position suggested that mutation pressure might influence the CUB. A highly significant correlation was observed between GC12 and GC3 (r = 0.910, p < 0.01), indicating that directional mutation affected all three codon positions across the genome. Translational selection (P2) and mutational responsive index (MRI) values of genes suggested that mutation plays a more important role than translational selection in members of the family Hepadnaviridae.
Identifiants
pubmed: 32036428
doi: 10.1007/s00705-020-04533-6
pii: 10.1007/s00705-020-04533-6
pmc: PMC7086886
doi:
Substances chimiques
RNA, Messenger
0
RNA, Viral
0
Viral Proteins
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
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