Codon bias is the nonuniform use of synonymous codons which encode the same amino acid. Some codons are more frequently used than others in several organisms, particularly in the highly expressed genes. The spectacular diversity of insects makes them a suitable candidate for analyzing the codon usage bias. Recent expansion in genome sequencing of different insect species provides an opportunity for studying the codon usage bias. Several works on patterns of codon usage bias were done on Drosophila and other related species but only few works were found in Hemiptera order. We analyzed codon usage in two Hemipteran insect species namely Bemisia tabaci and Homalodisca coagulata. Most frequent codons end with A or C at the 3rd codon position. The ENC (a measure of codon bias) value ranges from 43 to 60 (52.80) in B. tabaci but from 49 to 60 (56.69) in H. coagulata. In both insect species, a significant positive correlation was observed between A and A3%, C and C3%, and GC and GC3%, respectively. Our findings suggest that codon usage bias in two Hemipteran insect species is not remarkable and that mutation pressure causes the codon usage pattern in two Hemipteran insect species. 1. Introduction Codon usage bias is the phenomenon of unequal usage of codons during transcription and translation of genes to proteins. Some codons are used more often than alternate synonymous codons in genes where such bias exists. Such codons are often referred to as optimized codons or preferred codons. The extent of codon bias is mainly caused by mutation and translational selection [1–4]. Repeatedly used codons are often termed optimal or major codons, whereas less repeatedly used ones are termed nonoptimal or minor codons. Less repeatedly used codons usually correspond to less abundant tRNAs in the cell than optimal codons do [5–9] and the translational machinery is more likely to pause there [10]. During elongation stage of translation, these processing errors can occur in the cell and are termed as premature termination [10]. Therefore, the intensity of purifying selection is expected to increase as peptide elongation proceeds [9, 11] and so the codon usage bias in a gene should also lead to a steady increase [11]. In addition, optimal codons may be selected for translational effectiveness and so are more often used in highly articulated genes [2, 9, 12–16]. Therefore, codon usage bias may be accounted for by negative selection against nonoptimal codons and positive selection for optimal codons. Analysis of codon usage bias is a well-established technique for understanding
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