An extensive analysis on the global codon usage pattern of baculoviruses

An extensive analysis on the global codon usage pattern of baculoviruses Baculovirus-insect cell systems have been widely used over the past decades. However, few studies to date have addressed baculovirus codon usage. In this study, we calculated the effective number of codons (ENC) for all 5,842 ORFs from 42 completely sequenced baculoviruses. The results revealed that most of the baculoviruses lacked strong codon bias (ENC > 35). Exceptions were Lymantria dispar nucleopolyhedrovirus (LdMNPV) and Orgyia pseudotsugata nucleopolyhedrovirus (OpMNPV), which were found to have a strong codon bias (ENC < 35) in 20.9 and 11.8%, respectively, of their total genes. Comparisons of preferred codons based on taxonomic clades showed that the preferred codons were different in different clades, but nine codons (UUU, UAC, UUG, CAC, CAA, AAA, GUG, GAA, and AUU) were preferably adopted by most baculovirus genes. Correspondence analysis showed that the major trend in codon usage variation among all genes significantly correlated with the GC content of sequences. Analyses also suggested that the high condon bias of LdMNPV and OpMNPV were correlated with their high GC%. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Archives of Virology Springer Journals

An extensive analysis on the global codon usage pattern of baculoviruses

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Publisher
Springer Vienna
Copyright
Copyright © 2008 by Springer-Verlag
Subject
Biomedicine; Infectious Diseases; Medical Microbiology ; Virology
ISSN
0304-8608
eISSN
1432-8798
D.O.I.
10.1007/s00705-008-0260-1
Publisher site
See Article on Publisher Site

Abstract

Baculovirus-insect cell systems have been widely used over the past decades. However, few studies to date have addressed baculovirus codon usage. In this study, we calculated the effective number of codons (ENC) for all 5,842 ORFs from 42 completely sequenced baculoviruses. The results revealed that most of the baculoviruses lacked strong codon bias (ENC > 35). Exceptions were Lymantria dispar nucleopolyhedrovirus (LdMNPV) and Orgyia pseudotsugata nucleopolyhedrovirus (OpMNPV), which were found to have a strong codon bias (ENC < 35) in 20.9 and 11.8%, respectively, of their total genes. Comparisons of preferred codons based on taxonomic clades showed that the preferred codons were different in different clades, but nine codons (UUU, UAC, UUG, CAC, CAA, AAA, GUG, GAA, and AUU) were preferably adopted by most baculovirus genes. Correspondence analysis showed that the major trend in codon usage variation among all genes significantly correlated with the GC content of sequences. Analyses also suggested that the high condon bias of LdMNPV and OpMNPV were correlated with their high GC%.

Journal

Archives of VirologySpringer Journals

Published: Dec 1, 2008

References

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