Translation initiation AUG context varies with codon usage bias and gene length in Drosophila melanogaster

The relationship between the codon usage bias and the sequence context surrounding the AUG translation initiation codon was examined in 1100 Drosophila melanogaster mRNA sequences. The codon usage bias measured by the "codon adaptation index" (CAI), and the effectiveness of the AUG context for translation initiation assessed by the "AUG context adaptation index" (AUGCAI), showed a significant positive relationship (correlation coefficient: r = 0.34, p <0.0001), indicating that these two factors are evolutionally under a similar natural selection constraint at the translational level. The importance of each position of the AUG context in relation to codon usage bias was examined, and the preference for the nucleotide at the -13, -12, -11, -10, -7, -6, -5, -4, -3, -2, and -1 positions showed a significant positive correlation to the codon usage bias, suggesting the action of natural selection on these very specific positions of the Drosophila genome. The relationship between AUGCAI value and gene length was also examined, and a significant negative relationship was found (r = -0.15, p <0.0001), suggesting a general tendency of higher expressivity of shorter genes, and of lower expressivity of longer genes in D. melanogaster.