Analysis of Codon Usage Pattern and Prediction of Potentially Highly Expressed Genes in Drosophila

Abstract

Insecticide resistance development is one of the most serious concerns worldwide. The mechanism of this resistance has been attributed to evolutionary changes in pest/insect genomes such as alteration of drug target sites, up-regulation of degrading enzymes, and enhancement of drug excretion. In most of insects, this resistance is associated with higher amounts of insecticide detoxification enzymes as cytochrome P450s (CYPs), glutathione-stransferase (GSTs) and carboxylesterases (COEs). The main objective of this study is to apply synonymous codon usage bias to understand the expressivity level of different categories of resistant genes in model insect, Drosophila melanogaster. Codon usage of different detoxifying gene families was analyzed and a comparative analysis of codon usage and RSCU values was calculated. The high level of homogeneity is seen in different gene families of D. melanogaster. Codon usage of these gene families is mainly determined by compositional constraints however, translational selection is also operating in shaping the codon usage variation among the genes of different insects. The study reveals that G/C-ending codons are preferred over A/T-ending codons in highly expressed genes. This study also helps to develop new strategies to mitigate the insecticide resistance development in pest insects which is serious concern for agriculture and human health.