Exploring Codon Usage Patterns and Influencing Factors in Ranavirus DNA Polymerase Genes.
DNA polymerase
codon usage bias
mutation pressure
natural selection
ranavirus
Journal
Journal of basic microbiology
ISSN: 1521-4028
Titre abrégé: J Basic Microbiol
Pays: Germany
ID NLM: 8503885
Informations de publication
Date de publication:
04 Aug 2024
04 Aug 2024
Historique:
revised:
05
07
2024
received:
17
05
2024
accepted:
20
07
2024
medline:
5
8
2024
pubmed:
5
8
2024
entrez:
5
8
2024
Statut:
aheadofprint
Résumé
Ranaviruses, members of the genus Ranavirus within the family Iridoviridae, have become a significant concern for amphibian populations globally, along with other cold-blooded vertebrates, due to their emergence as a significant threat. We employed bioinformatics tools to examine the codon usage patterns in 61 DNA pol genes from Ranavirus, Lymphocystivirus, Megalocytivirus, and two unclassified ranaviruses, as no prior studies had been conducted on this topic. The results showed a slight or low level of codon usage bias (CUB) in the DNA pol genes of Ranavirus. Relative synonymous codon usage (RSCU) analysis indicated that the predominant codons favored in Ranavirus DNA pol genes terminate with C or G. Correlation analysis examining nucleotide content, third codon position, effective number of codons (ENC), correspondence analysis (COA), Aroma values, and GRAVY values indicated that the CUB across DNA pol genes could be influenced by both mutation pressure and natural selection. The neutrality plot indicated that natural selection is the primary factor driving codon usage. Furthermore, the analysis of the codon adaptation index (CAI) illustrated the robust adaptability of Ranavirus DNA pol genes to their hosts. Analysis of the relative codon deoptimization index (RCDI) suggested that Ranavirus DNA pol genes underwent greater selection pressure from their hosts. These findings will aid in comprehending the factors influencing the evolution and adaptation of Ranavirus to its hosts.
Identifiants
pubmed: 39099168
doi: 10.1002/jobm.202400289
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
e2400289Informations de copyright
© 2024 Wiley‐VCH GmbH.
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