An extensive analysis on the global codon usage pattern of baculoviruses

Area of Science:

• Molecular Biology
• Virology
• Bioinformatics

Background:

• Baculovirus-insect cell systems are established tools in biotechnology.
• Codon usage patterns in baculoviruses remain largely unexplored.
• Understanding codon bias is crucial for optimizing gene expression.

Purpose of the Study:

• To analyze codon usage patterns across a wide range of baculoviruses.
• To identify specific baculoviruses with significant codon bias.
• To investigate factors influencing codon usage variation in baculoviruses.

Main Methods:

• Calculated the effective number of codons (ENC) for 5,842 open reading frames (ORFs) from 42 complete baculovirus genomes.
• Compared preferred codons across different taxonomic clades.
• Utilized correspondence analysis to correlate codon usage with sequence characteristics like GC content.

Main Results:

• The majority of baculoviruses displayed a weak codon bias (ENC > 35).
• Lymantria dispar nucleopolyhedrovirus (LdMNPV) and Orgyia pseudotsugata nucleopolyhedrovirus (OpMNPV) showed strong codon bias in a portion of their genes (20.9% and 11.8%, respectively).
• A set of nine codons were preferentially used across most baculovirus genes.
• Codon usage variation significantly correlated with GC content, particularly in LdMNPV and OpMNPV.

Conclusions:

• Baculovirus codon usage is generally unbiased, with notable exceptions.
• GC content is a primary driver of codon usage variation in baculoviruses.
• Findings provide insights into baculovirus genome evolution and expression optimization.