Bioinformatics analysis of codon usage patterns and influencing factors in Penaeus monodon nudivirus

Tyagi, A, Singh, N, Gurtler, V and Karunasagar, I 2016, 'Bioinformatics analysis of codon usage patterns and influencing factors in Penaeus monodon nudivirus', Archives of Virology, vol. 161, no. 2, pp. 459-464.


Document type: Journal Article
Collection: Journal Articles

Title Bioinformatics analysis of codon usage patterns and influencing factors in Penaeus monodon nudivirus
Author(s) Tyagi, A
Singh, N
Gurtler, V
Karunasagar, I
Year 2016
Journal name Archives of Virology
Volume number 161
Issue number 2
Start page 459
End page 464
Total pages 6
Publisher Springer-Verlag
Abstract Penaeus monodon nudivirus (PmNV) is one of the most important and most commonly reported shrimp viruses. In the present study, codon usage of PmNV was studied in detail. Based on effective number of codons (ENC) values, strong to low codon usage bias was observed in PmNV genes. Nucleotide composition-ENC correlation analysis and the GC3 versus ENC relationship indicated that compositional constraint has a major effect on codon usage of PmNV. At the whole-genome level, relative synonymous codon usage (RSCU) analysis showed almost complete antagonism between the codon usage pattern of PmNV and its host P. monodon. However, codon adaptive index (CAI) values indicated that forces of selective/translational constraints have been able to overcome this antagonism in some genes.
Subject Biological Sciences not elsewhere classified
DOI - identifier 10.1007/s00705-015-2689-3
Copyright notice © Springer-Verlag Wien 2015
ISSN 0304-8608
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