Analysis of synonymous codon usage patterns in insect cypoviruses

Key Words：Effective number of codons, ENc-plot analysis, Neutrality plot analysis, Correspondence analysis, Preferred codons

Abstract：Cypoviruses (CPVs) are key regulatory factors of pest insect populations and are considered very promising biological control agents of pest insect populations. We detailed the synonymous codon usage patterns of seven CPVs through multivariate statistical methods. The result showed that CPV possessed a general weak synonymous usage bias. The codon usage patterns of most genes were constrained by base composition, while those of few minority genes were influenced by both base composition and other factors. Neutrality plot anaylsis revealed that selective pressures dominated over mutation in shapes base composition. Same electrophoretype CPVs shared more common preferred codons than same host CPVs. The 10 genome fragments within CPVs possessed statistically different codon biases. The codon biases of CPVs were significantly different from those of their insect host. All CPVs shared few common preferred codons with their host. Correspondence analysis further confirmed that base composition was the main factor influence synonymous codon usage and different electropherotype CPVs possessed different codon usage patterns. In the cluster analysis, same electropherotype CPVs possessed similar codon usage patterns, but same host CPVs possessed dissimilar codon usage patterns.